diff --git a/404.html b/404.html index 98fa415..95f53a6 100644 --- a/404.html +++ b/404.html @@ -18,6 +18,8 @@ + +

Page not found (404)

+ Content not found. Please use links in the navbar. +
+ +
+ + +
+ + + + + + diff --git a/articles/differential_signal_fixed.html b/articles/differential_signal_fixed.html index 030ab0f..425c96e 100644 --- a/articles/differential_signal_fixed.html +++ b/articles/differential_signal_fixed.html @@ -12,13 +12,14 @@ - + +
@@ -86,10 +93,16 @@

Stevie AdelaideJohn Curtin School of Medical Research, Australian National University
- Source: vignettes/differential_signal_fixed.Rmd + + + Source: vignettes/differential_signal_fixed.Rmd +

- 
+
+    
+    
+
 knitr::opts_chunk$set(message = FALSE, crop = NULL)

 

 
Introduction
@@ -721,7 +734,7 @@ 
Session Info
 sessionInfo()

-
## R version 4.4.0 (2024-04-24)
+
## R version 4.4.1 (2024-06-14)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -748,98 +761,98 @@ 
Session Info##  [1] quantro_1.38.0              here_1.0.1                 
 ##  [3] ggrepel_0.9.5               glue_1.7.0                 
 ##  [5] scales_1.3.0                plyranges_1.24.0           
-##  [7] extraChIPs_1.8.2            ggside_0.3.1               
-##  [9] patchwork_1.2.0             edgeR_4.2.0                
-## [11] limma_3.60.0                rtracklayer_1.64.0         
+##  [7] extraChIPs_1.8.3            ggside_0.3.1               
+##  [9] patchwork_1.2.0             edgeR_4.2.1                
+## [11] limma_3.60.4                rtracklayer_1.64.0         
 ## [13] BiocParallel_1.38.0         csaw_1.38.0                
 ## [15] SummarizedExperiment_1.34.0 Biobase_2.64.0             
 ## [17] MatrixGenerics_1.16.0       matrixStats_1.3.0          
-## [19] Rsamtools_2.20.0            Biostrings_2.72.0          
-## [21] XVector_0.44.0              GenomicRanges_1.56.0       
-## [23] GenomeInfoDb_1.40.0         IRanges_2.38.0             
-## [25] S4Vectors_0.42.0            BiocGenerics_0.50.0        
+## [19] Rsamtools_2.20.0            Biostrings_2.72.1          
+## [21] XVector_0.44.0              GenomicRanges_1.56.1       
+## [23] GenomeInfoDb_1.40.1         IRanges_2.38.1             
+## [25] S4Vectors_0.42.1            BiocGenerics_0.50.0        
 ## [27] lubridate_1.9.3             forcats_1.0.0              
 ## [29] stringr_1.5.1               dplyr_1.1.4                
 ## [31] purrr_1.0.2                 readr_2.1.5                
 ## [33] tidyr_1.3.1                 tibble_3.2.1               
 ## [35] ggplot2_3.5.1               tidyverse_2.0.0            
-## [37] BiocStyle_2.32.0           
+## [37] BiocStyle_2.32.1           
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] fs_1.6.4                   ProtGenerics_1.36.0       
 ##   [3] bitops_1.0-7               httr_1.4.7                
 ##   [5] RColorBrewer_1.1-3         doParallel_1.0.17         
 ##   [7] InteractionSet_1.32.0      doRNG_1.8.6               
-##   [9] tools_4.4.0                backports_1.4.1           
+##   [9] tools_4.4.1                backports_1.5.0           
 ##  [11] utf8_1.2.4                 R6_2.5.1                  
 ##  [13] HDF5Array_1.32.0           mgcv_1.9-1                
 ##  [15] lazyeval_0.2.2             Gviz_1.48.0               
 ##  [17] rhdf5filters_1.16.0        withr_3.0.0               
 ##  [19] prettyunits_1.2.0          gridExtra_2.3             
 ##  [21] base64_2.0.1               VennDiagram_1.7.3         
-##  [23] preprocessCore_1.66.0      cli_3.6.2                 
-##  [25] textshaping_0.3.7          formatR_1.14              
+##  [23] preprocessCore_1.66.0      cli_3.6.3                 
+##  [25] textshaping_0.4.0          formatR_1.14              
 ##  [27] labeling_0.4.3             sass_0.4.9                
 ##  [29] genefilter_1.86.0          askpass_1.2.0             
-##  [31] pkgdown_2.0.9.9000         systemfonts_1.1.0         
-##  [33] foreign_0.8-86             siggenes_1.78.0           
+##  [31] pkgdown_2.1.0.9000         systemfonts_1.1.0         
+##  [33] foreign_0.8-87             siggenes_1.78.0           
 ##  [35] illuminaio_0.46.0          dichromat_2.0-0.1         
 ##  [37] scrime_1.3.5               BSgenome_1.72.0           
-##  [39] rstudioapi_0.16.0          RSQLite_2.3.6             
+##  [39] rstudioapi_0.16.0          RSQLite_2.3.7             
 ##  [41] generics_0.1.3             BiocIO_1.14.0             
 ##  [43] Matrix_1.7-0               interp_1.1-6              
 ##  [45] futile.logger_1.4.3        fansi_1.0.6               
 ##  [47] abind_1.4-5                lifecycle_1.0.4           
-##  [49] yaml_2.3.8                 rhdf5_2.48.0              
-##  [51] SparseArray_1.4.3          BiocFileCache_2.12.0      
-##  [53] grid_4.4.0                 blob_1.2.4                
-##  [55] crayon_1.5.2               lattice_0.22-6            
+##  [49] yaml_2.3.9                 rhdf5_2.48.0              
+##  [51] SparseArray_1.4.8          BiocFileCache_2.12.0      
+##  [53] grid_4.4.1                 blob_1.2.4                
+##  [55] crayon_1.5.3               lattice_0.22-6            
 ##  [57] ComplexUpset_1.3.3         GenomicFeatures_1.56.0    
-##  [59] annotate_1.82.0            KEGGREST_1.44.0           
-##  [61] pillar_1.9.0               knitr_1.46                
+##  [59] annotate_1.82.0            KEGGREST_1.44.1           
+##  [61] pillar_1.9.0               knitr_1.48                
 ##  [63] beanplot_1.3.1             metapod_1.12.0            
 ##  [65] rjson_0.2.21               codetools_0.2-20          
 ##  [67] data.table_1.15.4          vctrs_0.6.5               
 ##  [69] png_0.1-8                  gtable_0.3.5              
-##  [71] cachem_1.1.0               xfun_0.44                 
-##  [73] S4Arrays_1.4.0             survival_3.6-4            
+##  [71] cachem_1.1.0               xfun_0.46                 
+##  [73] S4Arrays_1.4.1             survival_3.7-0            
 ##  [75] iterators_1.0.14           statmod_1.5.0             
-##  [77] GenomicInteractions_1.38.0 nlme_3.1-164              
+##  [77] GenomicInteractions_1.38.0 nlme_3.1-165              
 ##  [79] bit64_4.0.5                progress_1.2.3            
 ##  [81] filelock_1.0.3             rprojroot_2.0.4           
 ##  [83] bslib_0.7.0                nor1mix_1.3-3             
 ##  [85] rpart_4.1.23               colorspace_2.1-0          
-##  [87] DBI_1.2.2                  Hmisc_5.1-2               
+##  [87] DBI_1.2.3                  Hmisc_5.1-3               
 ##  [89] nnet_7.3-19                tidyselect_1.2.1          
-##  [91] bit_4.0.5                  compiler_4.4.0            
-##  [93] curl_5.2.1                 httr2_1.0.1               
-##  [95] htmlTable_2.4.2            xml2_1.3.6                
+##  [91] bit_4.0.5                  compiler_4.4.1            
+##  [93] curl_5.2.1                 httr2_1.0.2               
+##  [95] htmlTable_2.4.3            xml2_1.3.6                
 ##  [97] desc_1.4.3                 DelayedArray_0.30.1       
-##  [99] bookdown_0.39              checkmate_2.3.1           
+##  [99] bookdown_0.40              checkmate_2.3.1           
 ## [101] quadprog_1.5-8             rappdirs_0.3.3            
-## [103] digest_0.6.35              rmarkdown_2.27.1          
+## [103] digest_0.6.36              rmarkdown_2.27            
 ## [105] GEOquery_2.72.0            htmltools_0.5.8.1         
 ## [107] pkgconfig_2.0.3            jpeg_0.1-10               
 ## [109] base64enc_0.1-3            sparseMatrixStats_1.16.0  
-## [111] highr_0.10                 dbplyr_2.5.0              
+## [111] highr_0.11                 dbplyr_2.5.0              
 ## [113] fastmap_1.2.0              ensembldb_2.28.0          
-## [115] rlang_1.1.3                htmlwidgets_1.6.4         
+## [115] rlang_1.1.4                htmlwidgets_1.6.4         
 ## [117] UCSC.utils_1.0.0           DelayedMatrixStats_1.26.0 
 ## [119] farver_2.1.2               jquerylib_0.1.4           
 ## [121] jsonlite_1.8.8             mclust_6.1.1              
-## [123] VariantAnnotation_1.50.0   RCurl_1.98-1.14           
+## [123] VariantAnnotation_1.50.0   RCurl_1.98-1.16           
 ## [125] magrittr_2.0.3             Formula_1.2-5             
 ## [127] GenomeInfoDbData_1.2.12    Rhdf5lib_1.26.0           
-## [129] munsell_0.5.1              Rcpp_1.0.12               
+## [129] munsell_0.5.1              Rcpp_1.0.13               
 ## [131] stringi_1.8.4              zlibbioc_1.50.0           
-## [133] MASS_7.3-60.2              plyr_1.8.9                
-## [135] bumphunter_1.46.0          minfi_1.50.0              
-## [137] parallel_4.4.0             deldir_2.0-4              
-## [139] splines_4.4.0              multtest_2.60.0           
-## [141] hms_1.1.3                  locfit_1.5-9.9            
+## [133] MASS_7.3-61                bumphunter_1.46.0         
+## [135] plyr_1.8.9                 minfi_1.50.0              
+## [137] parallel_4.4.1             deldir_2.0-4              
+## [139] splines_4.4.1              multtest_2.60.0           
+## [141] hms_1.1.3                  locfit_1.5-9.10           
 ## [143] igraph_2.0.3               rngtools_1.5.2            
-## [145] biomaRt_2.60.0             futile.options_1.0.1      
-## [147] XML_3.99-0.16.1            evaluate_0.23             
+## [145] biomaRt_2.60.1             futile.options_1.0.1      
+## [147] XML_3.99-0.17              evaluate_0.24.0           
 ## [149] latticeExtra_0.6-30        biovizBase_1.52.0         
 ## [151] lambda.r_1.2.4             BiocManager_1.30.23       
 ## [153] tzdb_0.4.0                 foreach_1.5.2             
@@ -902,20 +915,32 @@ 
References
-        
-
+ +
+
+ + +
+ + + + + + diff --git a/articles/differential_signal_sliding.html b/articles/differential_signal_sliding.html index e9e039d..ce01391 100644 --- a/articles/differential_signal_sliding.html +++ b/articles/differential_signal_sliding.html @@ -12,13 +12,14 @@ - + +
@@ -86,10 +93,16 @@

Stevie AdelaideJohn Curtin School of Medical Research, Australian National University
- Source: vignettes/differential_signal_sliding.Rmd + + + Source: vignettes/differential_signal_sliding.Rmd +

- 
+
+    
+    
+
 knitr::opts_chunk$set(message = FALSE, crop = NULL)

 

 
Introduction
@@ -136,7 +149,7 @@ 
Installationpkg <- c(
   "tidyverse", "Rsamtools", "csaw", "BiocParallel", "rtracklayer", "edgeR", 
   "patchwork", "extraChIPs", "plyranges", "scales", "glue", "here", "quantro",
-  "cqn", "ggrepel", "BSgenome.Hsapiens.UCSC.hg19"
+  "ggrepel", "BSgenome.Hsapiens.UCSC.hg19"
 )
 BiocManager::install(pkg, update = FALSE)

Once these packages are installed, we can load them easily

@@ -155,7 +168,6 @@

Installationlibrary(here) library(magrittr) library(quantro) -library(cqn) library(ggrepel) theme_set(theme_bw())

@@ -481,15 +493,17 @@

Statistical TestingdualFilter() or may be normalised using any number of additional methods. In addition to the above -methods, a range-based \(H_0\) +methods, a range-based +H0H_0 (McCarthy and Smyth 2009) can be specified by providing a value to the fc or lfc arguments, which removes any need for post-hoc filtering and correctly controls the FDR, unlike post-hoc filtering based on a fold-change threshold.

Here, we’ll initially fit our data using Quasi-Likelihood Fits, library-size normalisation and setting a change in signal beyond the -range of \(\pm\) 20% as being of -interest. By default, the returned object, would be a +range of +±\pm +20% as being of interest. By default, the returned object, would be a SummarizedExperiment object containing the results from model fitting in the rowData() element. However, setting asRanges = TRUE will simply return the set of GRanges along @@ -513,12 +527,15 @@

Merging Windowskeyval_range.

For this vignette, we’ll merge using the asymptotically exact harmonic mean p-value, which can also be used for merging dependent -p-values (Wilson 2019). This approach tests H0: no \(p\)-value in the set of p-values is -significant. When merging windows using the harmonic mean p-values, -instead of values from a representative window, weighted averages for -the expression and logFC estimates are returned using the weights \(w_i = \frac{1}{p_i}\). A representative -window, corresponding to the original window with the lowest p-value is -returned.

+p-values (Wilson 2019). This approach tests H0: no +pp-value +in the set of p-values is significant. When merging windows using the +harmonic mean p-values, instead of values from a representative window, +weighted averages for the expression and logFC estimates are returned +using the weights +wi=1piw_i = \frac{1}{p_i}. +A representative window, corresponding to the original window with the +lowest p-value is returned.

 results_gr <- mergeByHMP(fit_gr, inc_cols = "overlaps_ref", merge_within = 120) %>% 
   addDiffStatus(drop = TRUE)
@@ -548,13 +565,14 @@ 
Merging Windows##   -------
 ##   seqinfo: 24 sequences from GRCh37 genome

In the above, we returned 19 ranges which we might consider using the -significance threshold \(\alpha\) = -0.05. As is common, we can assess our results using an MA plot. However, -given that testing is performed using sliding windows and merging -windows using the harmonic mean will introduce a bias, we can check -using the complete set of sliding windows and the final set of merged -windows. Any bias present in our data will be visible when using the -sliding windows, whilst our final results can be inspected using the +significance threshold +α\alpha += 0.05. As is common, we can assess our results using an MA plot. +However, given that testing is performed using sliding windows and +merging windows using the harmonic mean will introduce a bias, we can +check using the complete set of sliding windows and the final set of +merged windows. Any bias present in our data will be visible when using +the sliding windows, whilst our final results can be inspected using the merged windows.

 A <- fit_gr %>% 
@@ -1256,7 +1274,7 @@ 
Session Info
 sessionInfo()
-
## R version 4.4.0 (2024-04-24)
+
## R version 4.4.1 (2024-06-14)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -1276,116 +1294,114 @@ 
Session Info## tzcode source: system (glibc)
 ## 
 ## attached base packages:
-## [1] splines   stats4    stats     graphics  grDevices utils     datasets 
-## [8] methods   base     
+## [1] stats4    stats     graphics  grDevices utils     datasets  methods  
+## [8] base     
 ## 
 ## other attached packages:
-##  [1] ggrepel_0.9.5               cqn_1.50.0                 
-##  [3] quantreg_5.97               SparseM_1.81               
-##  [5] preprocessCore_1.66.0       nor1mix_1.3-3              
-##  [7] mclust_6.1.1                quantro_1.38.0             
-##  [9] magrittr_2.0.3              here_1.0.1                 
-## [11] glue_1.7.0                  scales_1.3.0               
-## [13] plyranges_1.24.0            extraChIPs_1.8.2           
-## [15] ggside_0.3.1                patchwork_1.2.0            
-## [17] edgeR_4.2.0                 limma_3.60.0               
-## [19] rtracklayer_1.64.0          BiocParallel_1.38.0        
-## [21] csaw_1.38.0                 SummarizedExperiment_1.34.0
-## [23] Biobase_2.64.0              MatrixGenerics_1.16.0      
-## [25] matrixStats_1.3.0           Rsamtools_2.20.0           
-## [27] Biostrings_2.72.0           XVector_0.44.0             
-## [29] GenomicRanges_1.56.0        GenomeInfoDb_1.40.0        
-## [31] IRanges_2.38.0              S4Vectors_0.42.0           
-## [33] BiocGenerics_0.50.0         lubridate_1.9.3            
-## [35] forcats_1.0.0               stringr_1.5.1              
-## [37] dplyr_1.1.4                 purrr_1.0.2                
-## [39] readr_2.1.5                 tidyr_1.3.1                
-## [41] tibble_3.2.1                ggplot2_3.5.1              
-## [43] tidyverse_2.0.0             BiocStyle_2.32.0           
+##  [1] ggrepel_0.9.5               quantro_1.38.0             
+##  [3] magrittr_2.0.3              here_1.0.1                 
+##  [5] glue_1.7.0                  scales_1.3.0               
+##  [7] plyranges_1.24.0            extraChIPs_1.8.3           
+##  [9] ggside_0.3.1                patchwork_1.2.0            
+## [11] edgeR_4.2.1                 limma_3.60.4               
+## [13] rtracklayer_1.64.0          BiocParallel_1.38.0        
+## [15] csaw_1.38.0                 SummarizedExperiment_1.34.0
+## [17] Biobase_2.64.0              MatrixGenerics_1.16.0      
+## [19] matrixStats_1.3.0           Rsamtools_2.20.0           
+## [21] Biostrings_2.72.1           XVector_0.44.0             
+## [23] GenomicRanges_1.56.1        GenomeInfoDb_1.40.1        
+## [25] IRanges_2.38.1              S4Vectors_0.42.1           
+## [27] BiocGenerics_0.50.0         lubridate_1.9.3            
+## [29] forcats_1.0.0               stringr_1.5.1              
+## [31] dplyr_1.1.4                 purrr_1.0.2                
+## [33] readr_2.1.5                 tidyr_1.3.1                
+## [35] tibble_3.2.1                ggplot2_3.5.1              
+## [37] tidyverse_2.0.0             BiocStyle_2.32.1           
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] fs_1.6.4                   ProtGenerics_1.36.0       
 ##   [3] bitops_1.0-7               httr_1.4.7                
 ##   [5] RColorBrewer_1.1-3         doParallel_1.0.17         
 ##   [7] InteractionSet_1.32.0      doRNG_1.8.6               
-##   [9] tools_4.4.0                backports_1.4.1           
+##   [9] tools_4.4.1                backports_1.5.0           
 ##  [11] utf8_1.2.4                 R6_2.5.1                  
 ##  [13] HDF5Array_1.32.0           lazyeval_0.2.2            
 ##  [15] Gviz_1.48.0                rhdf5filters_1.16.0       
 ##  [17] withr_3.0.0                prettyunits_1.2.0         
 ##  [19] gridExtra_2.3              base64_2.0.1              
-##  [21] VennDiagram_1.7.3          cli_3.6.2                 
-##  [23] textshaping_0.3.7          formatR_1.14              
-##  [25] sass_0.4.9                 genefilter_1.86.0         
-##  [27] askpass_1.2.0              pkgdown_2.0.9.9000        
-##  [29] systemfonts_1.1.0          foreign_0.8-86            
-##  [31] siggenes_1.78.0            illuminaio_0.46.0         
-##  [33] dichromat_2.0-0.1          scrime_1.3.5              
-##  [35] BSgenome_1.72.0            rstudioapi_0.16.0         
-##  [37] RSQLite_2.3.6              generics_0.1.3            
-##  [39] BiocIO_1.14.0              Matrix_1.7-0              
-##  [41] interp_1.1-6               futile.logger_1.4.3       
-##  [43] fansi_1.0.6                abind_1.4-5               
-##  [45] lifecycle_1.0.4            yaml_2.3.8                
-##  [47] rhdf5_2.48.0               SparseArray_1.4.3         
-##  [49] BiocFileCache_2.12.0       grid_4.4.0                
-##  [51] blob_1.2.4                 crayon_1.5.2              
-##  [53] lattice_0.22-6             ComplexUpset_1.3.3        
-##  [55] GenomicFeatures_1.56.0     annotate_1.82.0           
-##  [57] KEGGREST_1.44.0            pillar_1.9.0              
-##  [59] knitr_1.46                 beanplot_1.3.1            
-##  [61] metapod_1.12.0             rjson_0.2.21              
-##  [63] codetools_0.2-20           data.table_1.15.4         
-##  [65] vctrs_0.6.5                png_0.1-8                 
-##  [67] gtable_0.3.5               cachem_1.1.0              
-##  [69] xfun_0.44                  S4Arrays_1.4.0            
-##  [71] survival_3.6-4             iterators_1.0.14          
-##  [73] statmod_1.5.0              GenomicInteractions_1.38.0
-##  [75] nlme_3.1-164               bit64_4.0.5               
-##  [77] progress_1.2.3             filelock_1.0.3            
-##  [79] rprojroot_2.0.4            bslib_0.7.0               
-##  [81] rpart_4.1.23               colorspace_2.1-0          
-##  [83] DBI_1.2.2                  Hmisc_5.1-2               
-##  [85] nnet_7.3-19                tidyselect_1.2.1          
-##  [87] bit_4.0.5                  compiler_4.4.0            
-##  [89] curl_5.2.1                 httr2_1.0.1               
-##  [91] htmlTable_2.4.2            xml2_1.3.6                
-##  [93] desc_1.4.3                 DelayedArray_0.30.1       
-##  [95] bookdown_0.39              checkmate_2.3.1           
-##  [97] quadprog_1.5-8             rappdirs_0.3.3            
-##  [99] digest_0.6.35              rmarkdown_2.27.1          
-## [101] GEOquery_2.72.0            htmltools_0.5.8.1         
-## [103] pkgconfig_2.0.3            jpeg_0.1-10               
-## [105] base64enc_0.1-3            sparseMatrixStats_1.16.0  
-## [107] highr_0.10                 dbplyr_2.5.0              
-## [109] fastmap_1.2.0              ensembldb_2.28.0          
-## [111] rlang_1.1.3                htmlwidgets_1.6.4         
-## [113] UCSC.utils_1.0.0           DelayedMatrixStats_1.26.0 
-## [115] farver_2.1.2               jquerylib_0.1.4           
-## [117] jsonlite_1.8.8             VariantAnnotation_1.50.0  
-## [119] RCurl_1.98-1.14            Formula_1.2-5             
-## [121] GenomeInfoDbData_1.2.12    Rhdf5lib_1.26.0           
-## [123] munsell_0.5.1              Rcpp_1.0.12               
-## [125] stringi_1.8.4              zlibbioc_1.50.0           
-## [127] MASS_7.3-60.2              plyr_1.8.9                
-## [129] bumphunter_1.46.0          minfi_1.50.0              
-## [131] parallel_4.4.0             deldir_2.0-4              
-## [133] multtest_2.60.0            hms_1.1.3                 
-## [135] locfit_1.5-9.9             igraph_2.0.3              
-## [137] rngtools_1.5.2             biomaRt_2.60.0            
-## [139] futile.options_1.0.1       XML_3.99-0.16.1           
-## [141] evaluate_0.23              latticeExtra_0.6-30       
-## [143] biovizBase_1.52.0          lambda.r_1.2.4            
-## [145] BiocManager_1.30.23        tzdb_0.4.0                
-## [147] foreach_1.5.2              tweenr_2.0.3              
-## [149] MatrixModels_0.5-3         openssl_2.2.0             
-## [151] polyclip_1.10-6            reshape_0.8.9             
-## [153] ggforce_0.4.2              broom_1.0.6               
-## [155] xtable_1.8-4               restfulr_0.0.15           
-## [157] AnnotationFilter_1.28.0    ragg_1.3.2                
-## [159] memoise_2.0.1              AnnotationDbi_1.66.0      
-## [161] GenomicAlignments_1.40.0   cluster_2.1.6             
-## [163] timechange_0.3.0

+##  [21] VennDiagram_1.7.3          preprocessCore_1.66.0     
+##  [23] cli_3.6.3                  textshaping_0.4.0         
+##  [25] formatR_1.14               sass_0.4.9                
+##  [27] genefilter_1.86.0          askpass_1.2.0             
+##  [29] pkgdown_2.1.0.9000         systemfonts_1.1.0         
+##  [31] foreign_0.8-87             siggenes_1.78.0           
+##  [33] illuminaio_0.46.0          dichromat_2.0-0.1         
+##  [35] scrime_1.3.5               BSgenome_1.72.0           
+##  [37] rstudioapi_0.16.0          RSQLite_2.3.7             
+##  [39] generics_0.1.3             BiocIO_1.14.0             
+##  [41] Matrix_1.7-0               interp_1.1-6              
+##  [43] futile.logger_1.4.3        fansi_1.0.6               
+##  [45] abind_1.4-5                lifecycle_1.0.4           
+##  [47] yaml_2.3.9                 rhdf5_2.48.0              
+##  [49] SparseArray_1.4.8          BiocFileCache_2.12.0      
+##  [51] grid_4.4.1                 blob_1.2.4                
+##  [53] crayon_1.5.3               lattice_0.22-6            
+##  [55] ComplexUpset_1.3.3         GenomicFeatures_1.56.0    
+##  [57] annotate_1.82.0            KEGGREST_1.44.1           
+##  [59] pillar_1.9.0               knitr_1.48                
+##  [61] beanplot_1.3.1             metapod_1.12.0            
+##  [63] rjson_0.2.21               codetools_0.2-20          
+##  [65] data.table_1.15.4          vctrs_0.6.5               
+##  [67] png_0.1-8                  gtable_0.3.5              
+##  [69] cachem_1.1.0               xfun_0.46                 
+##  [71] S4Arrays_1.4.1             survival_3.7-0            
+##  [73] iterators_1.0.14           statmod_1.5.0             
+##  [75] GenomicInteractions_1.38.0 nlme_3.1-165              
+##  [77] bit64_4.0.5                progress_1.2.3            
+##  [79] filelock_1.0.3             rprojroot_2.0.4           
+##  [81] bslib_0.7.0                nor1mix_1.3-3             
+##  [83] rpart_4.1.23               colorspace_2.1-0          
+##  [85] DBI_1.2.3                  Hmisc_5.1-3               
+##  [87] nnet_7.3-19                tidyselect_1.2.1          
+##  [89] bit_4.0.5                  compiler_4.4.1            
+##  [91] curl_5.2.1                 httr2_1.0.2               
+##  [93] htmlTable_2.4.3            xml2_1.3.6                
+##  [95] desc_1.4.3                 DelayedArray_0.30.1       
+##  [97] bookdown_0.40              checkmate_2.3.1           
+##  [99] quadprog_1.5-8             rappdirs_0.3.3            
+## [101] digest_0.6.36              rmarkdown_2.27            
+## [103] GEOquery_2.72.0            htmltools_0.5.8.1         
+## [105] pkgconfig_2.0.3            jpeg_0.1-10               
+## [107] base64enc_0.1-3            sparseMatrixStats_1.16.0  
+## [109] highr_0.11                 dbplyr_2.5.0              
+## [111] fastmap_1.2.0              ensembldb_2.28.0          
+## [113] rlang_1.1.4                htmlwidgets_1.6.4         
+## [115] UCSC.utils_1.0.0           DelayedMatrixStats_1.26.0 
+## [117] farver_2.1.2               jquerylib_0.1.4           
+## [119] jsonlite_1.8.8             mclust_6.1.1              
+## [121] VariantAnnotation_1.50.0   RCurl_1.98-1.16           
+## [123] Formula_1.2-5              GenomeInfoDbData_1.2.12   
+## [125] Rhdf5lib_1.26.0            munsell_0.5.1             
+## [127] Rcpp_1.0.13                stringi_1.8.4             
+## [129] zlibbioc_1.50.0            MASS_7.3-61               
+## [131] bumphunter_1.46.0          plyr_1.8.9                
+## [133] minfi_1.50.0               parallel_4.4.1            
+## [135] deldir_2.0-4               splines_4.4.1             
+## [137] multtest_2.60.0            hms_1.1.3                 
+## [139] locfit_1.5-9.10            igraph_2.0.3              
+## [141] rngtools_1.5.2             biomaRt_2.60.1            
+## [143] futile.options_1.0.1       XML_3.99-0.17             
+## [145] evaluate_0.24.0            latticeExtra_0.6-30       
+## [147] biovizBase_1.52.0          lambda.r_1.2.4            
+## [149] BiocManager_1.30.23        tzdb_0.4.0                
+## [151] foreach_1.5.2              tweenr_2.0.3              
+## [153] openssl_2.2.0              polyclip_1.10-6           
+## [155] reshape_0.8.9              ggforce_0.4.2             
+## [157] broom_1.0.6                xtable_1.8-4              
+## [159] restfulr_0.0.15            AnnotationFilter_1.28.0   
+## [161] ragg_1.3.2                 memoise_2.0.1             
+## [163] AnnotationDbi_1.66.0       GenomicAlignments_1.40.0  
+## [165] cluster_2.1.6              timechange_0.3.0

References @@ -1463,20 +1479,32 @@

References - -

+ +

+ + + + + + + + + + diff --git a/articles/index.html b/articles/index.html index 025ceac..83ee8e8 100644 --- a/articles/index.html +++ b/articles/index.html @@ -3,6 +3,8 @@ + +
+ + +

Articles

+

All vignettes

+
extraChIPs: Differential Signal Using Fixed-Width Windows
extraChIPs: Differential Signal Using Sliding Windows
@@ -65,12 +75,22 @@

All vignettes

+ + + + + + + + diff --git a/articles/range_based_functions.html b/articles/range_based_functions.html index 2ae4adc..07a4de1 100644 --- a/articles/range_based_functions.html +++ b/articles/range_based_functions.html @@ -12,13 +12,14 @@ - + +
@@ -85,10 +92,16 @@

Stevie AdelaideJohn Curtin School of Medical Research, Australian National University
- Source: vignettes/range_based_functions.Rmd + + + Source: vignettes/range_based_functions.Rmd +

-
+ + + +

Introduction

This package is designed to enable the Gene Regulatory Analysis using @@ -230,7 +243,8 @@

Formation of Consensus Peaks## ------- ## seqinfo: 1 sequence from an unspecified genome; no seqlengths

However, we may wish for peaks to appear in all replicates, so we can -set the argument p = 1 (or any other value \(0 \leq p \leq 1\)).

+set the argument p = 1 (or any other value +0≤p≤10 \leq p \leq 1).

 makeConsensus(peaks, p = 1)
## GRanges object with 6 ranges and 3 metadata columns:
@@ -628,7 +642,7 @@ 
Session Info
 sessionInfo()

-
## R version 4.4.0 (2024-04-24)
+
## R version 4.4.1 (2024-06-14)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -652,38 +666,38 @@ 
Session Info## [8] base     
 ## 
 ## other attached packages:
-##  [1] plyranges_1.24.0            extraChIPs_1.8.2           
+##  [1] plyranges_1.24.0            extraChIPs_1.8.3           
 ##  [3] SummarizedExperiment_1.34.0 Biobase_2.64.0             
 ##  [5] MatrixGenerics_1.16.0       matrixStats_1.3.0          
-##  [7] ggside_0.3.1                GenomicRanges_1.56.0       
-##  [9] GenomeInfoDb_1.40.0         IRanges_2.38.0             
-## [11] S4Vectors_0.42.0            BiocGenerics_0.50.0        
+##  [7] ggside_0.3.1                GenomicRanges_1.56.1       
+##  [9] GenomeInfoDb_1.40.1         IRanges_2.38.1             
+## [11] S4Vectors_0.42.1            BiocGenerics_0.50.0        
 ## [13] BiocParallel_1.38.0         lubridate_1.9.3            
 ## [15] forcats_1.0.0               stringr_1.5.1              
 ## [17] dplyr_1.1.4                 purrr_1.0.2                
 ## [19] readr_2.1.5                 tidyr_1.3.1                
 ## [21] tibble_3.2.1                ggplot2_3.5.1              
-## [23] tidyverse_2.0.0             BiocStyle_2.32.0           
+## [23] tidyverse_2.0.0             BiocStyle_2.32.1           
 ## 
 ## loaded via a namespace (and not attached):
 ##   [1] BiocIO_1.14.0              bitops_1.0-7              
 ##   [3] filelock_1.0.3             polyclip_1.10-6           
-##   [5] XML_3.99-0.16.1            rpart_4.1.23              
-##   [7] lifecycle_1.0.4            httr2_1.0.1               
-##   [9] edgeR_4.2.0                MASS_7.3-60.2             
+##   [5] XML_3.99-0.17              rpart_4.1.23              
+##   [7] lifecycle_1.0.4            httr2_1.0.2               
+##   [9] edgeR_4.2.1                MASS_7.3-61               
 ##  [11] lattice_0.22-6             ensembldb_2.28.0          
-##  [13] backports_1.4.1            magrittr_2.0.3            
-##  [15] limma_3.60.0               Hmisc_5.1-2               
-##  [17] sass_0.4.9                 rmarkdown_2.27.1          
-##  [19] jquerylib_0.1.4            yaml_2.3.8                
+##  [13] backports_1.5.0            magrittr_2.0.3            
+##  [15] limma_3.60.4               Hmisc_5.1-3               
+##  [17] sass_0.4.9                 rmarkdown_2.27            
+##  [19] jquerylib_0.1.4            yaml_2.3.9                
 ##  [21] metapod_1.12.0             Gviz_1.48.0               
-##  [23] DBI_1.2.2                  RColorBrewer_1.1-3        
+##  [23] DBI_1.2.3                  RColorBrewer_1.1-3        
 ##  [25] abind_1.4-5                zlibbioc_1.50.0           
 ##  [27] AnnotationFilter_1.28.0    biovizBase_1.52.0         
-##  [29] RCurl_1.98-1.14            nnet_7.3-19               
+##  [29] RCurl_1.98-1.16            nnet_7.3-19               
 ##  [31] tweenr_2.0.3               VariantAnnotation_1.50.0  
 ##  [33] rappdirs_0.3.3             GenomeInfoDbData_1.2.12   
-##  [35] ggrepel_0.9.5              pkgdown_2.0.9.9000        
+##  [35] ggrepel_0.9.5              pkgdown_2.1.0.9000        
 ##  [37] codetools_0.2-20           DelayedArray_0.30.1       
 ##  [39] ggforce_0.4.2              xml2_1.3.6                
 ##  [41] tidyselect_1.2.1           futile.logger_1.4.3       
@@ -691,69 +705,81 @@ 
Session Info##  [45] ComplexUpset_1.3.3         BiocFileCache_2.12.0      
 ##  [47] base64enc_0.1-3            GenomicAlignments_1.40.0  
 ##  [49] jsonlite_1.8.8             Formula_1.2-5             
-##  [51] systemfonts_1.1.0          tools_4.4.0               
+##  [51] systemfonts_1.1.0          tools_4.4.1               
 ##  [53] progress_1.2.3             ragg_1.3.2                
-##  [55] Rcpp_1.0.12                glue_1.7.0                
-##  [57] gridExtra_2.3              SparseArray_1.4.3         
-##  [59] xfun_0.44                  withr_3.0.0               
+##  [55] Rcpp_1.0.13                glue_1.7.0                
+##  [57] gridExtra_2.3              SparseArray_1.4.8         
+##  [59] xfun_0.46                  withr_3.0.0               
 ##  [61] formatR_1.14               BiocManager_1.30.23       
 ##  [63] fastmap_1.2.0              latticeExtra_0.6-30       
-##  [65] fansi_1.0.6                digest_0.6.35             
+##  [65] fansi_1.0.6                digest_0.6.36             
 ##  [67] timechange_0.3.0           R6_2.5.1                  
-##  [69] textshaping_0.3.7          colorspace_2.1-0          
+##  [69] textshaping_0.4.0          colorspace_2.1-0          
 ##  [71] jpeg_0.1-10                dichromat_2.0-0.1         
-##  [73] biomaRt_2.60.0             RSQLite_2.3.6             
+##  [73] biomaRt_2.60.1             RSQLite_2.3.7             
 ##  [75] utf8_1.2.4                 generics_0.1.3            
 ##  [77] data.table_1.15.4          rtracklayer_1.64.0        
 ##  [79] prettyunits_1.2.0          InteractionSet_1.32.0     
 ##  [81] httr_1.4.7                 htmlwidgets_1.6.4         
-##  [83] S4Arrays_1.4.0             pkgconfig_2.0.3           
+##  [83] S4Arrays_1.4.1             pkgconfig_2.0.3           
 ##  [85] gtable_0.3.5               blob_1.2.4                
 ##  [87] XVector_0.44.0             htmltools_0.5.8.1         
-##  [89] bookdown_0.39              ProtGenerics_1.36.0       
+##  [89] bookdown_0.40              ProtGenerics_1.36.0       
 ##  [91] scales_1.3.0               png_0.1-8                 
-##  [93] knitr_1.46                 lambda.r_1.2.4            
+##  [93] knitr_1.48                 lambda.r_1.2.4            
 ##  [95] rstudioapi_0.16.0          tzdb_0.4.0                
 ##  [97] rjson_0.2.21               checkmate_2.3.1           
 ##  [99] curl_5.2.1                 cachem_1.1.0              
-## [101] parallel_4.4.0             foreign_0.8-86            
+## [101] parallel_4.4.1             foreign_0.8-87            
 ## [103] AnnotationDbi_1.66.0       restfulr_0.0.15           
 ## [105] desc_1.4.3                 pillar_1.9.0              
-## [107] grid_4.4.0                 vctrs_0.6.5               
+## [107] grid_4.4.1                 vctrs_0.6.5               
 ## [109] dbplyr_2.5.0               cluster_2.1.6             
-## [111] htmlTable_2.4.2            evaluate_0.23             
+## [111] htmlTable_2.4.3            evaluate_0.24.0           
 ## [113] VennDiagram_1.7.3          GenomicFeatures_1.56.0    
-## [115] cli_3.6.2                  locfit_1.5-9.9            
-## [117] compiler_4.4.0             futile.options_1.0.1      
-## [119] Rsamtools_2.20.0           rlang_1.1.3               
-## [121] crayon_1.5.2               interp_1.1-6              
+## [115] cli_3.6.3                  locfit_1.5-9.10           
+## [117] compiler_4.4.1             futile.options_1.0.1      
+## [119] Rsamtools_2.20.0           rlang_1.1.4               
+## [121] crayon_1.5.3               interp_1.1-6              
 ## [123] fs_1.6.4                   stringi_1.8.4             
 ## [125] deldir_2.0-4               munsell_0.5.1             
-## [127] Biostrings_2.72.0          lazyeval_0.2.2            
+## [127] Biostrings_2.72.1          lazyeval_0.2.2            
 ## [129] csaw_1.38.0                Matrix_1.7-0              
 ## [131] BSgenome_1.72.0            hms_1.1.3                 
 ## [133] patchwork_1.2.0            bit64_4.0.5               
-## [135] KEGGREST_1.44.0            statmod_1.5.0             
-## [137] highr_0.10                 igraph_2.0.3              
+## [135] KEGGREST_1.44.1            statmod_1.5.0             
+## [137] highr_0.11                 igraph_2.0.3              
 ## [139] broom_1.0.6                memoise_2.0.1             
 ## [141] bslib_0.7.0                bit_4.0.5                 
 ## [143] GenomicInteractions_1.38.0
+ + +
+
+ + + + + + + + + diff --git a/authors.html b/authors.html index b517f63..0928f03 100644 --- a/authors.html +++ b/authors.html @@ -3,6 +3,8 @@ + +
+ + +

Authors and Citation

+ +

  • Stevie Pederson. Author, maintainer.

    @@ -62,28 +72,43 @@

    Authors and Citation

    Citation

    - Source: DESCRIPTION + Source: DESCRIPTION
    + +

    Pederson S (2024). extraChIPs: Additional functions for working with ChIP-Seq data. -R package version 1.8.2, https://github.com/smped/extraChIPs. +R package version 1.8.3, https://github.com/smped/extraChIPs. 

    @Manual{,
   title = {extraChIPs: Additional functions for working with ChIP-Seq data},
   author = {Stevie Pederson},
   year = {2024},
-  note = {R package version 1.8.2},
+  note = {R package version 1.8.3},
   url = {https://github.com/smped/extraChIPs},
 }
    +
+
+ + +
+ + + + + + diff --git a/index.html b/index.html index e8c8f0b..3bd4a80 100644 --- a/index.html +++ b/index.html @@ -19,6 +19,8 @@ + +
@@ -102,6 +110,7 @@

Installation Instructions

+
+ +
+ + + + + + diff --git a/news/index.html b/news/index.html index 9ebbcac..5872530 100644 --- a/news/index.html +++ b/news/index.html @@ -3,6 +3,8 @@ + +
+ + +

Changelog

- Source: NEWS.md + Source: NEWS.md
+

Changes in version 0.99.0 (2022-03-28)

  • Submitted to Bioconductor
    • @@ -187,16 +196,28 @@

    Changes in 1.7

+ +
+ + + + + + + + diff --git a/pkgdown.yml b/pkgdown.yml index e7e811c..a4aa6e6 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -1,9 +1,8 @@ -pandoc: 3.1.13 -pkgdown: 2.0.9.9000 -pkgdown_sha: 5761658b7582743d0962136cd0c1e6e8d42b56d5 +pandoc: '3.2' +pkgdown: 2.1.0.9000 +pkgdown_sha: 2841c0f994fda7f7c7da94034bd24e3882fc7a37 articles: differential_signal_fixed: differential_signal_fixed.html differential_signal_sliding: differential_signal_sliding.html range_based_functions: range_based_functions.html -last_built: 2024-05-18T14:15Z - +last_built: 2024-07-22T17:07Z diff --git a/reference/addDiffStatus-methods.html b/reference/addDiffStatus-methods.html index 22dd077..fee4799 100644 --- a/reference/addDiffStatus-methods.html +++ b/reference/addDiffStatus-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Add a status column

- Source: R/addDiffStatus.R + Source: R/addDiffStatus.R
+

Add a status column based on significance and estimated change

+ 
addDiffStatus(x, ...)
 
@@ -89,34 +99,56 @@ 
Add a status column

 # S4 method for class 'SummarizedExperiment'
 addDiffStatus(x, ...)
+

Arguments

-
x
+ + +
x

Object to be classified

+ +
...

Used to pass arguments between methods

+ +
fc_col

Name of the fold-change column

+ +
sig_col

Name of the column with significance values

+ +
alpha

significance threshold

+ +
cutoff

minimum estimated change to be considered in either of the up or down categories

+ +
up, down, other

factor levels to annotate regions based on the above criteria

+ +
missing

Value to add when either fc_col or sig_col has NA values

+ +
new_col

name of the new column to be added

+ +
drop

logical(1) Drop unused factor levels from the status column

+

Value

-

An object of the same type as provided

+

An object of the same type as provided

Details

@@ -125,6 +157,7 @@

Details

Results in the new column will always be returned as a factor with levels in order of the values provided in the arguments other, down and up

+

Examples

## Working with a data.frame
@@ -182,12 +215,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/as_tibble.html b/reference/as_tibble.html index 9b5a0f2..4185609 100644 --- a/reference/as_tibble.html +++ b/reference/as_tibble.html @@ -3,6 +3,8 @@ + +
+ + +

Convert to a tibble

- Source: R/asTibble.R + Source: R/asTibble.R
+

Convert multiple Genomic objects to tibbles

+ 
# S3 method for class 'DataFrame'
 as_tibble(x, rangeAsChar = TRUE, ...)
@@ -77,24 +87,36 @@ 
Convert to a tibble

 # S3 method for class 'TopTags'
 as_tibble(x, ...)
+

Arguments

-
x
+ + +
x

A Genomic Ranges or DataFrame object

+ +
rangeAsChar

Convert any GRanges element to a character vector

+ +
...

Passed to tibble::as_tibble()

+ +
name

Name of column to use for ranges. Ignored if rangeAsChar = FALSE

+ +
suffix

Suffix appended to column names for anchor1 and anchor2 of a GInteractions object. Only used if specifying rangeAsChar = FALSE

+

Value

-

A tibble

+

A tibble

Details

@@ -114,6 +136,7 @@

Details

object, both anchors will returned with the default suffixes .x and .y

Defined as an S3 method for consistency with existing tidy methods

+

Examples

gr <- GRanges("chr1:1-10")
@@ -162,12 +185,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/bestOverlap-methods.html b/reference/bestOverlap-methods.html index 777d74e..014902b 100644 --- a/reference/bestOverlap-methods.html +++ b/reference/bestOverlap-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Find the best overlap between GRanges

- Source: R/AllGenerics.R, R/bestOverlap.R + Source: R/AllGenerics.R, R/bestOverlap.R
+

Find the best overlap between ranges

+ 
bestOverlap(x, y, ...)
 
@@ -82,28 +92,44 @@ 
Find the best overlap between GRanges

   ...
 )
+

Arguments

-
x
+ + +
x

a GRanges object

+ +
y

a named GRangesList or GRanges object with mcol as reference category

+ +
...

Not used

+ +
var

The variable to use as the category. Not required if y is a GRangesList

+ +
ignore.strand

logical(1) Passed to findOverlaps

+ +
missing

Value to assign to ranges with no overlap

+ +
min_prop

Threshold below which overlaps are discarded

+

Value

-

Character vector the same length as the supplied GRanges object

+

Character vector the same length as the supplied GRanges object

Details

@@ -116,6 +142,7 @@

Details

If the subject (y) is a GRangesList, the names of the list will be used to provide the best match

+

Examples

gr <- GRanges("chr1:1-10")
@@ -144,12 +171,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/chopMC.html b/reference/chopMC.html index 1a1dce8..9e43a9d 100644 --- a/reference/chopMC.html +++ b/reference/chopMC.html @@ -3,6 +3,8 @@ + +
+ + +

Keep unique ranges and collapse mcols

- Source: R/chopMC.R + Source: R/chopMC.R
+

Keep unique ranges by 'chopping' mcols

+ 
chopMC(x, simplify = TRUE)
+

Arguments

-
x
+ + +
x

A GenomicRanges object

+ +
simplify

logical(1)

+

Value

-

A GRanges object

+

A GRanges object

Details

@@ -80,6 +96,7 @@

Details

simplify = TRUE (the default). In this case, columns will be returned as vectors where possible.

+

Examples

gr <- GRanges(rep(c("chr1:1-10"), 2))
@@ -109,12 +126,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/colToRanges-methods.html b/reference/colToRanges-methods.html index ea97bc3..a78e8e5 100644 --- a/reference/colToRanges-methods.html +++ b/reference/colToRanges-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Coerce a column to a GRanges object

- Source: R/AllGenerics.R, R/colToRanges.R + Source: R/AllGenerics.R, R/colToRanges.R
+

Coerce a column to a GRanges object from a rectangular object

+ 
colToRanges(x, ...)
 
@@ -70,21 +80,31 @@ 
Coerce a column to a GRanges object

 # S4 method for class 'data.frame'
 colToRanges(x, var, seqinfo = NULL, ...)
+

Arguments

-
x
+ + +
x

A data-frame or GRanges object containing the column to coerce

+ +
...

Used to pass arguments to lower-level functions

+ +
var

The name of the column to coerce

+ +
seqinfo

A seqinfo object to be applied to the new GRanges object. Ignored if the column is already a GRanges object

+

Value

-

A GenomicRanges object

+

A GenomicRanges object

Details

@@ -96,6 +116,7 @@

Details

character column, this provides a simple method of coercion. In this case, no Seqinfo element will be applied to the GRanges element.

+

Examples

set.seed(73)
@@ -124,12 +145,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/collapseGenes.html b/reference/collapseGenes.html index 6ed5081..fa11ed2 100644 --- a/reference/collapseGenes.html +++ b/reference/collapseGenes.html @@ -3,6 +3,8 @@ + +
+ + +

Collapse a vector of gene names

- Source: R/collapseGenes.R + Source: R/collapseGenes.R
+

Collapse a vector of gene names

+ 
collapseGenes(
   x,
@@ -71,30 +81,50 @@ 
Collapse a vector of gene names

   ...
 )
+

Arguments

-
x
+ + +
x

character vector representing gene names

+ +
sort

logical(1) Should the names be sorted alphabetically

+ +
dedup

logical(1) Should duplicate names be removed

+ +
format

character string for markdown formatting of each element

+ +
sep

separator between vector elements

+ +
last

character string to place before the last element

+ +
numeric

logical(1) sort digits numerically, instead of as strings

+ +
width

The maximum width of the string before truncating to ...

+ +
...

passed to str_sort

+

Value

-

a glue object

+

a glue object

Details

@@ -102,6 +132,7 @@

Details

object of length 1. By default, symbols are deduplicated, sorted alpha-numerically and italicised with an underscore.

+

Examples

genes <- c("FOXP3", "BRCA1", "TP53")
@@ -115,12 +146,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/cytobands.html b/reference/cytobands.html index 580f76e..5ac22ae 100644 --- a/reference/cytobands.html +++ b/reference/cytobands.html @@ -3,6 +3,8 @@ + +
+ + +

Cytogenetic bands

- Source: R/data.R + Source: R/data.R
+

Cytogenetic bands for GRCh37/hg19 and GRCh38/hg38

+ 
data(grch37.cytobands)
 
 data(grch38.cytobands)
+

Format

Cytogenetic bands for standard chromosomes from GRCh37,in the format required by IdeogramTrack. A data.frame with 5 columns:

chrom

Chromosome

+
chromStart

Starting position for each cytogenetic band

+
chromEnd

End position for each cytogenetic band

+
name

Name for each band, e.g. p.36.33

+
gieStain

Staining pattern

+ +

An object of class data.frame with 862 rows and 5 columns.

+

Examples

data(grch37.cytobands)
@@ -112,12 +130,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/defineRegions.html b/reference/defineRegions.html index dbff426..e2f801d 100644 --- a/reference/defineRegions.html +++ b/reference/defineRegions.html @@ -3,6 +3,8 @@ + +
+ + +

Define Genomic Regions Based on Gene Annotations

- Source: R/defineRegions.R + Source: R/defineRegions.R
+

Use gene, transcript and exon annotations to define genomic regions

+ 
defineRegions(
   genes,
@@ -72,34 +82,52 @@ 
Define Genomic Regions Based on Gene Annotations

   ...
 )
+

Arguments

-
genes, transcripts, exons
+ + +
genes, transcripts, exons

GRanges objects defining each level of annotation

+ +
promoter

Numeric vector defining upstream and/or downstream distances for a promoter. Passing a single value will define a symmetrical promoter The first value represents the upstream range

+ +
upstream

The distance from a TSS defining an upstream promoter

+ +
intron

logical(1) Separate gene bodies into introns and exons. If intron = FALSE gene bodies will simply be defined as gene bodies

+ +
proximal

Distance from a gene to be considered a proximal intergenic region. If set to 0, intergenic regions will simply be considered as uniformly intergenic

+ +
simplify

Passed internally to reduceMC and setdiffMC

+ +
cols

Column names to be retained from the supplied annotations

+ +
...

Not used

+

Value

-

A GRangesList

+

A GRangesList

Details

@@ -118,6 +146,7 @@

Details

assumed that the gene/transcript/exon ranges will contain informative columns in the mcols() element.

+

Examples


@@ -199,12 +228,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/defineSeqinfo.html b/reference/defineSeqinfo.html index a8ffb84..b0b7a31 100644 --- a/reference/defineSeqinfo.html +++ b/reference/defineSeqinfo.html @@ -3,6 +3,8 @@ + +
+ + +

Use package data to define a Seqinfo object

- Source: R/defineSeqinfo.R + Source: R/defineSeqinfo.R
+

Use package data to define a Seqinfo object

+ 
defineSeqinfo(
   build = c("GRCh38", "GRCh37", "GRCm39", "GRCm38", "hg19", "hg38", "T2T-CHM13v2.0",
@@ -67,21 +77,31 @@ 
Use package data to define a Seqinfo object

   ...
 )
+

Arguments

-
build
+ + +
build

The Genome build used

+ +
chr

logical(1) Include the prefix "chr"

+ +
mito

Specify M or MT to include the mitochondrial chromosome. Omitted by default

+ +
...

Not used

+

Value

-

A Seqinfo object

+

A Seqinfo object

Details

@@ -91,6 +111,7 @@

Details

Currently implemented genome builds represent the four most common builds for ChIP-Seq analysis

+

Examples

defineSeqinfo("GRCh37", TRUE)
@@ -130,12 +151,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/distinctMC.html b/reference/distinctMC.html index 63c773c..573c785 100644 --- a/reference/distinctMC.html +++ b/reference/distinctMC.html @@ -3,6 +3,8 @@ + +
+ + +

Keep distinct ranges and mcols

- Source: R/distinctMC.R + Source: R/distinctMC.R
+

Keep distinct ranges by including mcols

+ 
distinctMC(x, ..., .keep_all = FALSE)
+

Arguments

-
x
+ + +
x

A GenomicRanges object

+ +
...

<data-masking> Passed to distinct

+ +
.keep_all

If TRUE, keep all columns in x

+

Value

-

A GRanges object

+

A GRanges object

Details

@@ -81,6 +99,7 @@

Details

the distinct combinations, in keeping with the dplyr function.

Will default to unique(granges(x)) if no columns are provided

+

Examples

gr <- GRanges(rep(c("chr1:1-10"), 2))
@@ -123,12 +142,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/dot-makeFinalProfileHeatmap.html b/reference/dot-makeFinalProfileHeatmap.html index b5098c8..4bb2d84 100644 --- a/reference/dot-makeFinalProfileHeatmap.html +++ b/reference/dot-makeFinalProfileHeatmap.html @@ -3,6 +3,8 @@ + +
+ + +

Make a profile heatmap

- Source: R/plotProfileHeatmap.R + Source: R/plotProfileHeatmap.R
+

Make a profile heatmap with optional summary panel at the top

+ 
.makeFinalProfileHeatmap(
   data,
@@ -78,47 +88,78 @@ 
Make a profile heatmap

   ...
 )
+

Arguments

-
data
+ + +
data

A data.frame or tibble in long form

+ +
x, y

The values mapped to the x & y axes

+ +
fill

The column used for heatmap colours

+ +
colour, linetype

Columns used for the summary plot in the top panel

+ +
facet_x, facet_y

Columns used to facet the plot along these axes

+ +
summary_fun

Function used to create the summary value at each position

+ +
rel_height

The relative height of the top panel

+ +
x_lab, y_lab, fill_lab

_labels added to x/y-axes & the fill legend

+ +
...

Passed to facet_grid

+

Value

-

A ggplot2 object

+

A ggplot2 object

Details

The workhorse function for generating the final heatmap Expects a single data.frame in long form with requisite columns

+
+ +
+ + + + + + diff --git a/reference/dot-mapFeatures.html b/reference/dot-mapFeatures.html index 2e58a48..dbc647a 100644 --- a/reference/dot-mapFeatures.html +++ b/reference/dot-mapFeatures.html @@ -3,6 +3,8 @@ + +
+ + +

Map ranges to genes using features as an anchor

- Source: R/mapByFeature.R + Source: R/mapByFeature.R
+

Map ranges to genes using features as an anchor

+ 
.mapFeatures(.gr, .feat, .genes, .cols, .gr2feat, .feat2gene, ...)
+

Arguments

-
.gr
+ + +
.gr

The ranges to map onto

+ +
.feat

Features to use for mapping

+ +
.genes

GRanges object containing gene-level information

+ +
.cols

The columns from .genes to map onto .gr

+ +
.gr2feat

The maximum distance between ranges and features

+ +
.feat2gene

The maximum distance between features & genes

+ +
...

Passed to findOverlaps and subsetByOverlaps

+

Value

-

A data.frame

+

A data.frame

+
+ +
+ + + + + + diff --git a/reference/dot-mapGi.html b/reference/dot-mapGi.html index c31d288..de82f6f 100644 --- a/reference/dot-mapGi.html +++ b/reference/dot-mapGi.html @@ -3,6 +3,8 @@ + +
+ + +

Map ranges to genes via Interactions

- Source: R/mapByFeature.R + Source: R/mapByFeature.R
+

Map ranges to genes via Interactions

+ 
.mapGi(.gr, .gi, .genes, .cols, .gr2gi, .gi2gene, ...)
+

Arguments

-
.gr
+ + +
.gr

The ranges to map onto

+ +
.gi

GInteractions object

+ +
.genes

GRanges object containing gene-level information

+ +
.cols

The columns from .genes to map onto .gr

+ +
.gr2gi

The maximum distance between ranges and anchors

+ +
.gi2gene

The maximum distance between anchors & genes

+ +
...

Passed to findOverlaps

+

Value

-

data.frame of mapped ranges

+

data.frame of mapped ranges

+
+ +
+ + + + + + diff --git a/reference/dot-mapWithin.html b/reference/dot-mapWithin.html index 59060bf..94c6fb5 100644 --- a/reference/dot-mapWithin.html +++ b/reference/dot-mapWithin.html @@ -3,6 +3,8 @@ + +
+ + +

Map ranges to all genes within a set distance

- Source: R/mapByFeature.R + Source: R/mapByFeature.R
+

Map ranges to all genes within a set distance

+ 
.mapWithin(.gr, .genes, .cols, .within, ...)
+

Arguments

-
.gr
+ + +
.gr

The ranges to map onto

+ +
.genes

GRanges object containing gene-level information

+ +
.cols

The columns from .genes to map onto .gr

+ +
.within

The maximum distance between ranges & genes

+ +
...

Passed to findOverlaps

+

Value

-

A data.frame

+

A data.frame

+
+ +
+ + + + + + diff --git a/reference/dualFilter.html b/reference/dualFilter.html index 6ade196..d1f535c 100644 --- a/reference/dualFilter.html +++ b/reference/dualFilter.html @@ -3,6 +3,8 @@ + +
+ + +

Apply two filters to sliding windows

- Source: R/dualFilter.R + Source: R/dualFilter.R
+

Apply two filters to counts generated using sliding windows

+ 
dualFilter(
   x,
@@ -71,37 +81,57 @@ 
Apply two filters to sliding windows

   BPPARAM = bpparam()
 )
+

Arguments

-
x
+ + +
x

RangedSummarizedExperiment containing sample counts

+ +
bg

RangedSummarizedExperiment containing background/input counts, or alternate method for selecting samples from within x, such as a logical, numeric or character vector

+ +
ref

GRanges object containing ranges where signal is expected

+ +
q

The upper percentile of the reference ranges expected to be returned when tuning the filtering criteria

+ +
logCPM

logical(1) Add a logCPM assay to the returned data

+ +
keep.totals

logical(1) Keep the original library sizes or replace using only the retained windows

+ +
bin.size

Bin sizes when calling filterWindowsControl. If not specified will default to the largest of 2000bp or 10x the window size

+ +
prior.count

Passed to filterWindowsControl and filterWindowsProportion

+ +
BPPARAM

Settings for running in parallel

+

Value

-

A RangedSummarizedExperiment which is a +

A RangedSummarizedExperiment which is a filtered subset of the original object. If requested the assay "logCPM" will be added (TRUE by default)

@@ -131,6 +161,7 @@

Details

machine or file structure to that which the original sliding windows were prepared. Please see the example/vignette for runnable code.

+

Examples

# \donttest{
@@ -245,12 +276,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/ex_datasets.html b/reference/ex_datasets.html index 748a705..28fd5c6 100644 --- a/reference/ex_datasets.html +++ b/reference/ex_datasets.html @@ -3,19 +3,28 @@ visualisation strategies. Generation of all datasets is documented in system.file("script/ex_datasets.md", package = "extraChIPs") + ex_genes Simple GRanges object with complete ranges for each gene + ex_trans Exon &amp; transcript level information prepared for plotting with Gviz or plotHFGC() + ex_prom Regions defined as promoters + ex_hic Example HiC interactions + + + '> + +
+ + +

Datasets for an example region

- Source: R/data.R + Source: R/data.R
+

Various example datasets for demonstrating analysis and visualisation strategies. @@ -75,14 +91,20 @@

Datasets for an example region

system.file("script/ex_datasets.md", package = "extraChIPs")

ex_genes

Simple GRanges object with complete ranges for each gene

+
ex_trans

Exon & transcript level information prepared for plotting with Gviz or plotHFGC()

+
ex_prom

Regions defined as promoters

+
ex_hic

Example HiC interactions

+ +
+ 
data(ex_trans)
 
@@ -92,6 +114,7 @@ 
Datasets for an example region

 
 data(ex_hic)
+

Format

GRanges and GInteractions objects

@@ -100,6 +123,7 @@

Format

An object of class GRanges of length 9.

An object of class GInteractions of length 1.

+

Examples

data(ex_trans)
@@ -153,12 +177,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/extraChIPs-package.html b/reference/extraChIPs-package.html index 875c369..0414155 100644 --- a/reference/extraChIPs-package.html +++ b/reference/extraChIPs-package.html @@ -5,6 +5,8 @@ + +
+ + +

extraChIPs: A package for enabling and extending ChIP-Seq analysis

- Source: R/extraChIPs.R + Source: R/extraChIPs.R
+

The package provides three categories of important functions: Range-based, Visualisation and Convenience functions, with most centred around GenomicRanges objects

+ +

Range-based Functions

+ + +

Many of the range-based functions included in this package have a focus on retaining the mcols information whilst manipulating the ranges, such as reduceMC() which not only reduces the Ranges, but collapses the mcols @@ -90,6 +104,8 @@

Range-based Functions

Visualisation Functions

+ +

  • plotHFGC() is a wrapper to Gviz plotting functions, able to take any combination of HiC, Features, Genes and Coverage (i.e. BigWig) and plot a specified range.

    • @@ -105,6 +121,8 @@

    Visualisation Functions

Convenience Functions

+ +

  • fitAssayDiff() enables differential signal analysis on a SummarizedExperiment object

  • collapseGenes() prints a vector of genes for an rmarkdown document, @@ -126,17 +144,28 @@

    See also

    Author

    Stevie Pederson

+
+ +
+ + + + + + diff --git a/reference/fitAssayDiff-methods.html b/reference/fitAssayDiff-methods.html index d2023d2..e5f7155 100644 --- a/reference/fitAssayDiff-methods.html +++ b/reference/fitAssayDiff-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Detect Differential ChIP Signal

- Source: R/fitAssayDiff.R + Source: R/fitAssayDiff.R
+

Detect differential ChIP signal using one of many approaches

+ 
fitAssayDiff(x, ...)
 
@@ -79,64 +89,98 @@ 
Detect Differential ChIP Signal

   ...,
   null = c("interval", "worst.case"),
   robust = FALSE,
-  type = "apeglm"
+  type = c("apeglm", "ashr", "normal")
 )
+

Arguments

-
x
+ + +
x

a SummarizedExperiment object

+ +
...

Passed to normLibSizes and

+ +
assay

The assay to use for analysis

+ +
design

The design matrix to use for analysis

+ +
coef

The required column from the design matrix

+ +
lib.size

The column within the colData element which contains the library size information. If set to NULL, column summaries will be used.

+ +
method

the analytic method to be used. Can be 'qlf' which will fit counts using the glmQLFit strategy , or 'lt' which fits the limma-trend model on logCPM, or pre-processed logCPM values. Setting method = 'wald' will call nbinomWaldTest

+ +
norm

The normalisation strategy to use when running the glmQLF model or the Wald test. The value 'none' relies solely on library-size normalisation, and is the default. All methods available in normLibSizes are implemented. Ignored when using method = "lt"

+ +
groups

character(1) If a column name is supplied here, group-based normalisation will be applied to GLM models treating data in this column as a grouping factor. Ignored when using method = "lt"

+ +
fc, lfc

Thresholds passed to treat, glmTreat or lfcShrink

+ +
asRanges

logical(1). By default, the returned object will be a SummarizedExperiment object with the results added to the rowData element. Setting asRanges = TRUE will only return the GRanges object from this element

+ +
offset

If provided will be used as the offset when a DGEList object is created during model fitting for method = 'qlf'

+ +
weighted

logical(1) Passed to normLibSizes. Only used when applying a TMM-type normalisation strategy

+ +
null

Passed to glmTreat glmQLFit when method = "qlf". If method = "lt", instead passed to lmFit

+ +
robust

Passed to treat and eBayes

+ +
type

Passed to lfcShrink

+

Value

-

A SummarizedExperiment object with results set as the rowData element. +

A SummarizedExperiment object with results set as the rowData element. Any existing columns not contained in the differential ChIP results will be retained. Results from testing will contain logCPM, logFC, PValue and any t/F @@ -165,13 +209,15 @@

Details

called by column name. No normalisation is applied when using the limma-trend model, as this allows for previous normalisation strategies to be performed on the data.

-

When applying the nbinomWaldTest, without groups and using -colSums for library sizes (instead of total alignments), the standard -normalisation factors from estimateSizeFactorsForMatrix will -be used. In all other scenarios, normalisation factors as returned by +

When applying the nbinomWaldTest, applying RLE normalisation +without groups, and using colSums for library sizes (instead of total +alignments), the standard normalisation factors from +estimateSizeFactors will be used. +In all other scenarios, normalisation factors as returned by normLibSizes will be used. The fitType is set to 'local' when estimating dispersions, and this can be -easily modified by passing fitType via the dot arguments.

+easily modified by passing fitType via the dot arguments. +Results are additionally returned after applying lfcShrink.

Normalising to ChIP Input samples is not yet implemented. Similarly, the use of offsets when applying the Wald test is not yet implemented.

@@ -186,6 +232,7 @@

Details

if requiring intermediate output from any steps, then these can be run individually as conventionally specified.

+

Examples

nrows <- 200; ncols <- 6
@@ -226,12 +273,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/fixed_width_datasets.html b/reference/fixed_width_datasets.html index 6aa8ff9..95b9aef 100644 --- a/reference/fixed_width_datasets.html +++ b/reference/fixed_width_datasets.html @@ -5,6 +5,8 @@ + +
+ + +

Datasets for the Fixed-Width Vignette

- Source: R/data.R + Source: R/data.R
+

GRangesList of peaks and SummarizedExperiment of counts All were saved during initial vignette preparation at https://github.com/smped/extraChIPs_vignette/blob/main/differential_signal_fixed.Rmd

+ 
data(se)
 
 data(peaks)
+

Format

An object of class RangedSummarizedExperiment with 188 rows and 6 columns.

An object of class CompressedGRangesList of length 6.

+

Examples

data(se)
@@ -127,12 +139,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/getProfileData-methods.html b/reference/getProfileData-methods.html index 44e54a0..7de201b 100644 --- a/reference/getProfileData-methods.html +++ b/reference/getProfileData-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Get Profile Data surrounding specified ranges

- Source: R/AllGenerics.R, R/getProfileData.R + Source: R/AllGenerics.R, R/getProfileData.R
+

Get coverage Profile Data surrounding specified ranges

+ 
getProfileData(x, gr, ...)
 
@@ -102,38 +112,62 @@ 
Get Profile Data surrounding specified ranges

   ...
 )
+

Arguments

-
x
+ + +
x

A BigWigFile or BigWiFileList

+ +
gr

A GRanges object

+ +
...

Passed to normalizeToMatrix

+ +
upstream

The distance to extend upstream from the centre of each range within gr

+ +
downstream

The distance to extend downstream from the centre of each range within gr

+ +
bins

The total number of bins to break the extended ranges into

+ +
mean_mode

The method used for calculating the score for each bin. See normalizeToMatrix for details

+ +
log

logical(1) Should the returned values be log2-transformed

+ +
offset

Value added to data if log-transforming. Ignored otherwise

+ +
n_max

Upper limit on the number of ranges to return profile data for. By default, no limit will be applied .

+ +
BPPARAM

Passed internally to bplapply

+

Value

-

GRanges or GrangesList with column profile_data, as described above

+

GRanges or GrangesList with column profile_data, as described above

Details

@@ -153,6 +187,7 @@

Details

default. To run in parallel pass a MulticoreParam object to the BPPARAM argument.

+

Examples

bw <- system.file("tests", "test.bw", package = "rtracklayer")
@@ -190,12 +225,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/grlToSE-methods.html b/reference/grlToSE-methods.html index d816532..5bb646b 100644 --- a/reference/grlToSE-methods.html +++ b/reference/grlToSE-methods.html @@ -4,6 +4,8 @@ + +
+ + +

Set columns from a GRangesList as Assays in a SummarizedExperiment

- Source: R/AllGenerics.R, R/grlToSE.R + Source: R/AllGenerics.R, R/grlToSE.R
+

Move one or more columns from a GRangesList elements into assays in a RangesSummarizedEperiment

+ 
grlToSE(x, ...)
 
@@ -74,27 +84,43 @@ 
Set columns from a GRangesList as Assays in a SummarizedExperiment

   ignore.strand = FALSE
 )
+

Arguments

-
x
+ + +
x

A GrangesList

+ +
...

Passed to reduce

+ +
assayCols

Columns to move to separate assays

+ +
metaCols

Columns to move to mcols within the rowRanges element

+ +
keyvals

The value to use when choosing representative values

+ +
by

How to choose by keyvals

+ +
ignore.strand

logical(1). Whether the strand of the input ranges should be ignored or not.

+

Value

-

A RangedSummarizedExperiment

+

A RangedSummarizedExperiment

Details

@@ -109,6 +135,7 @@

Details

the value provided as the keyvals, taking either the min or max value in this column as the representative range.

+

Examples

a <- GRanges("chr1:1-10")
@@ -158,12 +185,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/importPeaks.html b/reference/importPeaks.html index 932a655..fa63898 100644 --- a/reference/importPeaks.html +++ b/reference/importPeaks.html @@ -3,6 +3,8 @@ + +
+ + +

Import peaks

- Source: R/importPeaks.R + Source: R/importPeaks.R
+

Import peaks in narrowPeak, broadPeak or bed format

+ 
importPeaks(
   x,
@@ -73,39 +83,63 @@ 
Import peaks

   ...
 )
+

Arguments

-
x
+ + +
x

One or more files to be imported. All files must be of the same type, i.e. narrow or broad

+ +
type

The type of peaks to be imported

+ +
blacklist

A set of ranges to be excluded

+ +
seqinfo

A seqinfo object to be applied to the GRanges objects

+ +
pruning.mode

How to handle conflicts if supplying a seqinfo object. Defaults to pruning.mode = "coarse". Only "coarse" and "error" are implemented. See seqinfo.

+ +
sort

logical. Should the ranges be sorted during import

+ +
setNames

logical Set basename(x) as the name for each element of the GRangesList

+ +
glueNames

glue syntax for naming list elements

+ +
centre

Add the estimated peak centre. Ignored unless type = "narrow"

+ +
nameRanges

Place any values in the name column as range names within each file.

+ +
...

passed to sort

+

Value

-

A GRangesList

+

A GRangesList

Details

@@ -113,6 +147,7 @@

Details

GenomicRanges objects.

If importing bed files, only the default 3-6 columns will imported.

+

Examples

fl <- system.file(
@@ -188,12 +223,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/index.html b/reference/index.html index c2cbc3c..5907c5e 100644 --- a/reference/index.html +++ b/reference/index.html @@ -3,6 +3,8 @@ + +
+ + +

Reference

+

Overview

@@ -238,16 +247,27 @@

Data Objects

Datasets for the Fixed-Width Vignette
+
+ +
+ + + + + + diff --git a/reference/makeConsensus.html b/reference/makeConsensus.html index 6eb0b64..88cf25a 100644 --- a/reference/makeConsensus.html +++ b/reference/makeConsensus.html @@ -3,6 +3,8 @@ + +
+ + +

Make a set of consensus peaks

- Source: R/makeConsensus.R + Source: R/makeConsensus.R
+

Make a set of consensus peaks based on the number of replicates

+ 
makeConsensus(
   x,
@@ -71,32 +81,48 @@ 
Make a set of consensus peaks

   ...
 )
+

Arguments

-
x
+ + +
x

A GRangesList

+ +
p

The minimum proportion of samples (i.e. elements of x) required for a peak to be retained in the output. By default all merged peaks will be returned

+ +
var

Additional columns in the mcols element to retain

+ +
method

Either return the union of all overlapping ranges, or the regions within the overlapping ranges which are covered by the specified proportion of replicates. When using p = 0, both methods will return identical results

+ +
ignore.strand, simplify, ...

Passed to reduceMC or intersectMC internally

+ +
min_width

Discard any regions below this width

+ +
merge_within

Passed to reduce as min.gapwidth

+

Value

-

GRanges object with mcols containing a logical vector for every element of +

GRanges object with mcols containing a logical vector for every element of x, along with the column n which adds all logical columns. These columns denote which replicates contain an overlapping peak for each range

If any additional columns have been requested using var, these will be @@ -121,6 +147,7 @@

Details

See also

reduceMC intersectMC

+

Examples

data("peaks")
@@ -228,12 +255,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/mapByFeature.html b/reference/mapByFeature.html index faf7d96..dbf6326 100644 --- a/reference/mapByFeature.html +++ b/reference/mapByFeature.html @@ -3,6 +3,8 @@ + +
+ + +

Map Genomic Ranges to genes using defined features

- Source: R/mapByFeature.R + Source: R/mapByFeature.R
+

Map Genomic Ranges to genes using defined regulatory features

+ 
mapByFeature(
   gr,
@@ -76,52 +86,82 @@ 
Map Genomic Ranges to genes using defined features

   ...
 )
+

Arguments

-
gr
+ + +
gr

GRanges object with query ranges to be mapped to genes

+ +
genes

GRanges object containing genes (or any other nominal feature) to be assigned

+ +
prom

GRanges object defining promoters

+ +
enh

GRanges object defining Enhancers

+ +
gi

GInteractions object defining interactions. Mappings from interactions to genes should be performed as a separate prior step.

+ +
cols

Column names to be assigned as mcols in the output. Columns must be minimally present in genes. If all requested columns are found in any of prom, enh or gi, these pre-existing mappings will be preferentially used. Any columns not found in utilised reference objects will be ignored.

+ +
gr2prom

The maximum permissible distance between a query range and any ranges defined as promoters

+ +
gr2enh

The maximum permissible distance between a query range and any ranges defined as enhancers

+ +
gr2gi

The maximum permissible distance between a query range and any ranges defined as GInteraction anchors

+ +
gr2gene

The maximum permissible distance between a query range and genes (for ranges not otherwise mapped)

+ +
prom2gene

The maximum permissible distance between a range provided in prom and a gene

+ +
enh2gene

The maximum permissible distance between a range provided in enh and a gene

+ +
gi2gene

The maximum permissible distance between a GInteractions anchor (provided in gi) and a gene

+ +
...

Passed to findOverlaps and overlapsAny internally

+

Value

-

A GRanges object with added mcols as specified

+

A GRanges object with added mcols as specified

Details

@@ -149,6 +189,7 @@

Details

prom, enh or gi objects, this will be used in preference to any obtained from the genes object.

+

Examples

## Define some genes
@@ -223,12 +264,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/mapGrlCols.html b/reference/mapGrlCols.html index fa6f2bc..4179888 100644 --- a/reference/mapGrlCols.html +++ b/reference/mapGrlCols.html @@ -4,6 +4,8 @@ + +
+ + +

Collapse a GRangesList adding multiple columns from each element

- Source: R/mapGrlCols.R + Source: R/mapGrlCols.R
+

Make consensus peaks and add individual columns from each original GRangesList element

+ 
mapGrlCols(
   x,
@@ -71,27 +81,43 @@ 
Collapse a GRangesList adding multiple columns from each element

   ...
 )
+

Arguments

-
x
+ + +
x

GRangesList

+ +
var

Column(s) to map onto the set of consensus peaks

+ +
collapse

Columns specified here will be simplified into a single column. Should only be character or factor columns

+ +
collapse_sep,

String to separate values when collapsing columns

+ +
name_sep

String to separate values when adding column names

+ +
include

logical(1) Include the original ranges as character columns

+ +
...

Passed to makeConsensus

+

Value

-

GRanges object with a set of consensus ranges across all list +

GRanges object with a set of consensus ranges across all list elements and values from each element mapped to these consensus ranges.

If requested (include = TRUE) the original ranges are returned as character columns, as there will be multiple NA values in each.

@@ -101,6 +127,7 @@

Details

Starting with a GRangesList, make a single GRanges object with select columns from each element added to the new object

+

Examples

a <- GRanges(paste0("chr1:", seq(1, 61, by = 20)))
@@ -168,12 +195,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/mergeByCol-methods.html b/reference/mergeByCol-methods.html index 0d840c8..d7da362 100644 --- a/reference/mergeByCol-methods.html +++ b/reference/mergeByCol-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Merge sliding windows using a specified column

- Source: R/mergeByCol.R + Source: R/mergeByCol.R
+

Merge sliding windows using a specified column

+ 
mergeByCol(x, ...)
 
@@ -92,41 +102,67 @@ 
Merge sliding windows using a specified column

   ...
 )
+

Arguments

-
x
+ + +
x

A GenomicRanges or SummarizedExperiment object

+ +
...

Not used

+ +
df

A data.frame-like object containing the columns of interest. If not provided, any columns in the mcols() slot will be used.

+ +
col

The column to select as representative of the merged ranges

+ +
by

The method for selecting representative values

+ +
logfc

Column containing logFC values

+ +
pval

Column containing p-values

+ +
inc_cols

Any additional columns to return. Output will always include columns specified in the arguments col, logfc and pval. Note that values from any additional columns will correspond to the selected range returned in keyval_range

+ +
p_adj_method

Any of p.adjust.methods

+ +
merge_within

Merge any ranges within this distance

+ +
ignore_strand

Passed internally to reduce and findOverlaps

+ +
min_win

Only keep merged windows derived from at least this number

+

Value

-

A Genomic Ranges object

+

A Genomic Ranges object

Details

@@ -152,6 +188,7 @@

Details

If called on a SummarizedExperiment object, the function will be applied to the rowRanges element.

+

Examples

x <- GRanges(c("chr1:1-10", "chr1:6-15", "chr1:51-60"))
@@ -199,12 +236,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/mergeByHMP-methods.html b/reference/mergeByHMP-methods.html index 4fd13b2..13225d3 100644 --- a/reference/mergeByHMP-methods.html +++ b/reference/mergeByHMP-methods.html @@ -4,6 +4,8 @@ + +
+ + +

Merge Sliding Windows using the Harmonic Mean P

- Source: R/mergeByHMP.R + Source: R/mergeByHMP.R
+

Merge overlapping windows using harmonic mean p-values from significance testing

+ 
mergeByHMP(x, ...)
 
@@ -97,48 +107,74 @@ 
Merge Sliding Windows using the Harmonic Mean P

   ...
 )
+

Arguments

-
x
+ + +
x

GenomicRanges object

+ +
...

Not used

+ +
df

data.frame with results of differential binding analysis performed using a sliding window strategy. If not provided, the columns in the mcols() element of x will be used

+ +
w

vector of weights to applied when calculating harmonic mean p-values

+ +
logfc, pval, cpm

Column names for the values holding window specific estimates of change in binding (logfc), overall signal intensity (cpm) and the significance from statistical testing (pval).

+ +
inc_cols

(Optional) Character vector of any additional columns in df to return. Values will correspond to the range in the keyval_range column

+ +
p_adj_method

One of p.adjust.methods or "fwer". If "fwer" is specified the adjusted harmonic-mean p-value will be returned in a form which strictly controls the experiment-wide FWER. Please see vignette("harmonicmeanp") for more details

+ +
merge_within

Merge any non-overlapping windows within this distance

+ +
ignore_strand

Passed internally to reduce and findOverlaps

+ +
min_win

Only keep merged windows derived from at least this number

+ +
keyval

Return the key-value range as the window associated with the minimum p-value, or by merging the ranges from all windows with raw p-values below the merged harmonic-mean p-value

+ +
hm_pre

Prefix to add to the beginning of all HMP-derived columns

+

Value

-

A GenomicRanges object with merged ranges from the original object along with +

A GenomicRanges object with merged ranges from the original object along with summarised or representative values from the relevant columns. The range corresponding to a representative values is also returned as described above

@@ -167,6 +203,7 @@

Details

An additional column with adjusted hmp-values is returned with the suffix '_*' added where the p-value adjustment method is added after the underscore.

+

Examples

x <- GRanges(c("chr1:1-10", "chr1:6-15", "chr1:51-60"))
@@ -214,12 +251,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/mergeBySig-methods.html b/reference/mergeBySig-methods.html index b0c589f..d652013 100644 --- a/reference/mergeBySig-methods.html +++ b/reference/mergeBySig-methods.html @@ -4,6 +4,8 @@ + +
+ + +

Merge overlapping ranges based on p-values

- Source: R/mergeBySig.R + Source: R/mergeBySig.R
+

Merge overlapping windows using p-values from significance testing

+ 
mergeBySig(x, ...)
 
@@ -96,42 +106,66 @@ 
Merge overlapping ranges based on p-values

   ...
 )
+

Arguments

-
x
+ + +
x

GenomicRanges object

+ +
...

Passed to all csaw functions being wrapped

+ +
df

data.frame with results of differential binding analysis performed using a sliding window strategy. If not provided, the columns in the mcols() element of x will be used

+ +
logfc, pval, cpm

Column names for the values holding window specific estimates of change in binding (logfc), overall signal intensity (cpm) and the significance from statistical testing (pval)

+ +
inc_cols

(Optional) Character vector of any additional columns in df to return

+ +
p_adj_method

One of p.adjust.methods

+ +
alpha

Significance threshold to apply during internal calculations

+ +
method

Shorthand versions for which csaw strategy to use for merging windows. Choose from 'combine' (combineTests), 'best' (getBestTest) or 'minimal' (minimalTests).

+ +
merge_within

Merge any non-overlapping windows within this distance

+ +
ignore_strand

Passed internally to reduce and findOverlaps

+ +
min_win

Only keep merged windows derived from at least this number

+

Value

-

A GenomicRanges object with overlapping ranges from the original object +

A GenomicRanges object with overlapping ranges from the original object merged and representative values returned. The range corresponding to the representative values is also returned

@@ -150,6 +184,7 @@

Details

the same name as the original but with the suffix '_*' added where the p-value adjustment method is added after the underscore.

+

Examples

x <- GRanges(c("chr1:1-10", "chr1:6-15", "chr1:51-60"))
@@ -200,12 +235,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/partitionRanges-methods.html b/reference/partitionRanges-methods.html index 246c883..66a4885 100644 --- a/reference/partitionRanges-methods.html +++ b/reference/partitionRanges-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Partition a set of Genomic Ranges

- Source: R/AllGenerics.R, R/partitionRanges.R + Source: R/AllGenerics.R, R/partitionRanges.R
+

Partition a set of Genomic Ranges by another

+ 
partitionRanges(x, y, ...)
 
@@ -72,27 +82,41 @@ 
Partition a set of Genomic Ranges

   ...
 )
+

Arguments

-
x, y
+ + +
x, y

GenomicRanges objects

+ +
...

Not used

+ +
y_as_both

logical(1) If there are any unstranded regions in y, should these be assigned to both strands. If TRUE unstranded regions can be used to partition stranded regions

+ +
ignore.strand

If set to TRUE, then the strand of x and y is set to "*" prior to any computation.

+ +
simplify

Pass to chopMC and simplify mcols in the output

+ +
suffix

Added to any shared column names in the provided objects

+

Value

-

A GRanges object

+

A GRanges object

Details

@@ -101,6 +125,7 @@

Details

The complete set of mcols from both initial objects will included in the set of partitioned ranges

+

Examples

x <- GRanges(c("chr1:1-10", "chr1:6-15"))
@@ -142,12 +167,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotAssayDensities-methods.html b/reference/plotAssayDensities-methods.html index e5c7db9..5a26093 100644 --- a/reference/plotAssayDensities-methods.html +++ b/reference/plotAssayDensities-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Plot Densities for any assay within a SummarizedExperiment

- Source: R/plotAssayDensities.R + Source: R/plotAssayDensities.R
+

Plot Densities for any assay within a SummarizedExperiment

+ 
plotAssayDensities(x, ...)
 
@@ -73,32 +83,50 @@ 
Plot Densities for any assay within a SummarizedExperiment

   ...
 )
+

Arguments

-
x
+ + +
x

A SummarizedExperiment object

+ +
...

Passed to density

+ +
assay

An assay within x

+ +
colour

Optional column in colData to colour lines by. To remove any colours, set this argument to NULL

+ +
linetype

Any optional column in colData used to determine linetype

+ +
group

Used by geom_line. Defaults to the sample names but setting to NULL will over-write this and only groups specified by colour or linetype will be drawn

+ +
trans

character(1). Any transformative function to be applied to the data before calculating the density, e.g. trans = "log2"

+ +
n_max

Maximum number of points to use when calculating densities

+

Value

-

A ggplot2 object. Scales and labels can be added using conventional +

A ggplot2 object. Scales and labels can be added using conventional ggplot2 syntax.

@@ -106,6 +134,7 @@

Details

Uses ggplot2 to create a density plot for all samples within the selected assay

+

Examples

data("se")
@@ -127,12 +156,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotAssayHeatmap-methods.html b/reference/plotAssayHeatmap-methods.html index a0db084..008637a 100644 --- a/reference/plotAssayHeatmap-methods.html +++ b/reference/plotAssayHeatmap-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Draw a heatmap from a single SummarizedExperiment assay

- Source: R/plotAssayHeatmap.R + Source: R/plotAssayHeatmap.R
+

Use ggplot2 to create a heatmap from a SummarizedExperiment object

+ 
plotAssayHeatmap(x, ...)
 
@@ -74,37 +84,57 @@ 
Draw a heatmap from a single SummarizedExperiment assay

   ...
 )
+

Arguments

-
x
+ + +
x

a SummarizedExperiment object

+ +
...

Not used

+ +
assay

the assay to take values from

+ +
by_x

the parameter to use for the x-axis. Will default to column names but should be one value per sample, such as an additional column containing shortened sample labels.

+ +
facet_x

column from colData(x) which will be used to group samples along the x-axis

+ +
ysideline

logical(1) Draw a line across the side of the y-axis summarising values for each range

+ +
yside_col

column from colData(x) to group and colour the lines drawn on the side of the y-axis. If grouping by treatment or replicate, the mean values will be shown

+ +
trans

character(1). Any transformative function to be applied to the data before calculating the density, e.g. trans = "log2"

+ +
n_max

Maximum number of ranges to draw

+

Value

-

A ggplot2 object. Scales and labels can be added using conventional +

A ggplot2 object. Scales and labels can be added using conventional ggplot2 syntax.

@@ -123,6 +153,7 @@

Details

heatmap creation using scale_fill_\* for the main heatmap, and scale_colour_\* for any groupings along the y-axis

+

Examples

nrows <- 10; ncols <- 4
@@ -145,12 +176,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotAssayPCA-methods.html b/reference/plotAssayPCA-methods.html index 569a099..b100c19 100644 --- a/reference/plotAssayPCA-methods.html +++ b/reference/plotAssayPCA-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Plot PCA For any assay within a SummarizedExperiment

- Source: R/plotAssayPCA.R + Source: R/plotAssayPCA.R
+

Plot PCA for any assay within a SummarizedExperiment object

+ 
plotAssayPCA(x, ...)
 
@@ -79,42 +89,70 @@ 
Plot PCA For any assay within a SummarizedExperiment

   ...
 )
+

Arguments

-
x
+ + +
x

An object containing an assay slot

+ +
...

Passed to geom_text

+ +
assay

The assay to perform PCA on

+ +
colour

The column name to be used for colours

+ +
shape, size

The column name(s) to be used for determining the shape or size of points

+ +
label

The column name to be used for labels

+ +
show_points

logical(1). Display the points. If TRUE any labels will repel. If FALSE, labels will appear at the exact points

+ +
pc_x

numeric(1) The PC to plot on the x-axis

+ +
pc_y

numeric(1) The PC to plot on the y-axis

+ +
trans

character(1). Any transformative function to be applied to the data before performing the PCA, e.g. trans = "log2"

+ +
n_max

Subsample the data to this many points before performing PCA

+ +
tol

Any rows with variance below this value will be excluded prior to passing to prcomp. All rows are scaled and centred by default

+ +
rank

Passed to prcomp

+

Value

-

A ggplot2 object

+

A ggplot2 object

Details

@@ -122,6 +160,7 @@

Details

transformation prior to performing the PCA can be specified using the trans argument

+

Examples

data("se")
@@ -148,12 +187,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotAssayRle-methods.html b/reference/plotAssayRle-methods.html index fedd947..6cb5b47 100644 --- a/reference/plotAssayRle-methods.html +++ b/reference/plotAssayRle-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Plot RLE for a given assay within a SummarizedExperiment

- Source: R/AllGenerics.R, R/plotAssayRle.R + Source: R/AllGenerics.R, R/plotAssayRle.R
+

Plot RLE for a given assay within a SummarizedExperiment

+ 
plotAssayRle(x, ...)
 
@@ -74,33 +84,53 @@ 
Plot RLE for a given assay within a SummarizedExperiment

   ...
 )
+

Arguments

-
x
+ + +
x

A SummarizedExperiment object

+ +
...

Passed to geom_boxplot

+ +
assay

The assay to plot

+ +
colour

Column from colData(x) to outline the boxplots

+ +
fill

Column from colData(x) to fill the boxplots

+ +
rle_group

Column from colData(x) to calculate RLE within groups Commonly an alternative sample label.

+ +
by_x

Boxplots will be drawn by this grouping variable from colData(x). If not specified, the default values will be colnames(x)

+ +
n_max

Maximum number of points to plot

+ +
trans

character(1). Numerical transformation to apply to the data prior to RLE calculation

+

Value

-

A ggplot2 object

+

A ggplot2 object

Details

@@ -108,6 +138,7 @@

Details

transformation prior to performing the RLE can be specified using the trans argument

+

Examples

data("se")
@@ -130,12 +161,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotGrlCol.html b/reference/plotGrlCol.html index 4bb6ba8..371fbea 100644 --- a/reference/plotGrlCol.html +++ b/reference/plotGrlCol.html @@ -3,6 +3,8 @@ + +
+ + +

Draw a plot from a GRangesList column

- Source: R/plotGrlCol.R + Source: R/plotGrlCol.R
+

Draw a plot from a GRangesList column using ggplot2

+ 
plotGrlCol(
   x,
@@ -81,55 +91,89 @@ 
Draw a plot from a GRangesList column

   digits = 0
 )
+

Arguments

-
x
+ + +
x

A GRangesList

+ +
var

The variable to plot. Either a column in the mcols element or width. Can be quoted or unquoted

+ +
geom

Choose between different geoms, or even provide a geom_*() function

+ +
.id

The column name to place the element names. Passed internally to the same argument in bind_rows

+ +
df

Optional data.frame with columns to be passed to the colour or fill parameters. Must contain a column with the same name as the value passed to the .id argument.

+ +
fill, colour

Optional column names found in the df. Can be quoted or unquoted

+ +
q

The overall percentile to be drawn as a labelled, horizontal line. Set q = 0 to hide this line

+ +
q_size

Text size of percentile label

+ +
qline_type, qline_col

Linetype and colour arguments for the horizontal line showing the specified percentile(s)

+ +
total

Glue syntax for totals, representing the length of each GRangesList element

+ +
total_geom

Passed to annotate. Set to none to hide totals

+ +
total_pos

Position for placing totals

+ +
total_size, total_alpha

Size and transparency of totals

+ +
total_adj

Adjustment for labels

+ +
...

Passed to the geom if selecting via character string. Ignored otherwise

+ +
digits

Number of decimal places for the horizontal line label

+

Value

-

A ggplot object

+

A ggplot object

Details

@@ -149,6 +193,7 @@

Details

able to be placed across the median values, or at the top and bottom extremes of the plot.

+

Examples

## Load some peaks
@@ -189,12 +234,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotHFGC.html b/reference/plotHFGC.html index 1926ec4..8c41308 100644 --- a/reference/plotHFGC.html +++ b/reference/plotHFGC.html @@ -3,6 +3,8 @@ + +
+ + +

Plot a Genomic Region showing HiC, Features, Genes and Coverage

- Source: R/plotHFGC.R + Source: R/plotHFGC.R
+

Plot a region with showing HiC, Features, Genes and Coverage

+ 
plotHFGC(
   gr,
@@ -99,24 +109,35 @@ 
Plot a Genomic Region showing HiC, Features, Genes and Coverage

   title.width = 1.5
 )
+

Arguments

-
gr
+ + +
gr

The range(s) of interest. Must be on a single chromosome

+ +
hic

Any HiC interactions to be included as a GenomicInteractions object. If not supplied, no HiC track will be drawn.

+ +
features

A named GRangesList or list of GRangesList objects. Each GRangesList should contain features in each element which will drawn on the same track. If providing a list, each GRangesList within the list will drawn on a separate track. If this argument is not specified, no feature track will be drawn. Features will be drawn with colours provided in featcol.

+ +
genes

A GRanges object with exon structure for each transcript/gene. If not included, no track will be drawn for gene/transcript structure. The expected mcols in this object are type, gene, exon transcript and symbol. See data(ex_trans) for an example.

+ +
coverage

A named list of BigWigFileList objects containing the primary tracks to show coverage for. Each list element will be drawn on a @@ -124,92 +145,147 @@

Arguments

track. List names will become track names. Alternatively, a single BigWigFileList will plot all individual files on separate tracks. If not included, no coverage tracks will be drawn.

+ +
annotation

Annotations for the coverage track(s). A single GRangesList if coverage is a BigWigListList. If coverage is supplied as a list of BigWigFileLists, a named list of GRangesList objects for each coverage track being annotatated. Names must match those given for coverage.

+ +
zoom

Multiplicative factor for zooming in and out

+ +
shift

Shift the plot. Applied after zooming

+ +
max

The maximum width of the plotting region. Given that the width of the final plotting window will be determined by any HiC interactions, this argument excludes any interactions beyond this distance. Plotting can be somewhat slow if any long range interactions are included. Ignored if no HiC interactions are supplied.

+ +
axistrack

logical. Add an AxisTrack()

+ +
cytobands

Cytogenetic bands to be displayed on each chromosome. See data('grch37.cytobands') for the correct format. Only drawn if a cytobands data.frame is provided.

+ +
covtype

The plot type for coverage. Currently only lines ("l") and heatmaps ("heatmap") are supported

+ +
linecol

If passing a BigWigFileList to coverage, a vector of colours. If passing a list of BigWigFileList objects to coverage, a list of colours with structure that matches the object being passed to coverage, i.e. a named list of the same length, with elements who's length matches each BigWigFileList. Only used if covtype = "l".

+ +
gradient

Colour gradient for heatmaps

+ +
hiccol

list with names "anchors" and "interactions". Colours are passed to these elements

+ +
featcol

Named vector (or list) of colours for each feature. Must be provided if drawing features

+ +
genecol

Named vector (or list) of colours for each gene category

+ +
annotcol

Colours matching the coverage annotations

+ +
highlight

Outline colour for the highlight track. Setting this to NULL will remove the highlight

+ +
hicsize, featsize, genesize, covsize, annotsize

Relative sizes for each track (hic, features, genes, coverage & annotation)

+ +
hicname, featname

Names displayed in the LHS panel

+ +
featstack

Stacking for the fature track

+ +
collapseTranscripts

Passed to GeneRegionTrack for the genes track. Defaults to "auto" for automatic setting. If the number of transcripts to be plotted is > maxtrans, the argument will be automatically set to "meta", otherwise this will be passed as FALSE which will show all transcripts.

+ +
maxTrans

Only used if collapseTranscripts is set to "auto".

+ +
ylim

If a numeric vector, this will be passed to all coverage tracks. Alternatively, a named list of y-limits for each coverage track with names that match those in each element of the coverage list.

+ +
...

Passed to DataTrack for the coverage tracks only. Useful arguments may be things like legend

+ +
fontsize

Applied across all tracks

+ +
cex.title

Passed to all tracks

+ +
rotation.title

Passed to all tracks

+ +
col.title

Passed to all tracks

+ +
background.title

Passed to all tracks

+ +
title.width

Expansion factor passed to plotTracks, and used to widen the panels on the LHS of all tracks. Can have unpredictable effects on the font size of y-axis limits due to the algorithm applied by plotTracks

+

Value

-

A Gviz object

+

A Gviz object

Details

@@ -245,6 +321,9 @@

Details

Displaying HiC Interactions

+ + +

The available arguments for displaying HiC Interactions are defined below. If hic is supplied, a single InteractionTrack will be added displaying @@ -256,20 +335,29 @@

Displaying HiC Interactions

hic

This is the GInteractions object required for inclusion of a HiC track in the final output. Will be ignored if not supplied

+
hiccol

Determines the colours used for display of anchors and interactions

+
hicsize

Relative size of the track compared to others

+
hicname

The name to display on the LHS panel

+
max

The maximum width of the plotted region. If multiple long-range interactions are identified, this provides an upper limit for the display. This defaults to 10Mb.

+ +

Displaying Features

+ + +

If wanting to add an AnnotationTrack with regions defined as 'features', the following arguments are highly relevant. All are ignored if features is not provided.

@@ -277,18 +365,27 @@

Displaying Features

A named GRangesList. Each element will be considered as a separate feature and drawn as a block in a distinct colour. Any mcols data will be ignored.

+
featcol

A named vector (or list) providing a colour for each element of features

+
featname

The name to display on the LHS panel

+
featstack

Stacking to be applied to all supplied features

+
featsize

Relative size of the track compared to others

+ +

Displaying Genes And Transcripts

+ + +

To display genes or transcripts, simply provide a single GRanges object if you wish to display all genes on a single track. The mcols element of this object should contain the columns feature, @@ -303,19 +400,27 @@

Displaying Genes And Transcripts

object is supplied to this argument.

genes

A GRanges or GRangesList object as described above

+
genecol

A single colour if supplying a GRanges object, or a named vector/list of colours matching the GRangesList

+
genesize

Relative size of the track compared to others

+
collapseTranscripts

Passed to all tracks. See the GeneRegionTrack section in settings for detail regarding possible arguments. If genes is a GRangesList, can be a named vector/list with names matching the names of the genes object.

+ +

Displaying Coverage Tracks

+ + +

This section contains the most flexibility and can take two types of input. The first option is a BigWigFileList, which will lead to each BigWig file being plotted on it's own track. @@ -337,10 +442,12 @@

Displaying Coverage Tracks

as a separate track, with any BigWig files overlaid using the same y-axis. The list must be named with these names displayed on the LHS panel. Each internal BigWig within a BigWigFileList must also be named.

+
covtype

Currently only lines (covtype = "l") and heatmaps (covtype = "heatmap") are supported. Colours can be specified using the arguments below

+
linecol

Can be a single colour applied to all tracks, or a named vector (or list) of colours. If coverage is a single BigWigFileList, @@ -349,16 +456,20 @@

Displaying Coverage Tracks

a list with matching names. Each element of this list should also be a named vector with names that exactly match those of each corresponding BigWigFileList.

+
gradient

A colour gradient applied to all heatmap tracks. No specific structure is required beyond a vector of colours.

+
covsize

Relative size of the tracks compared to others

+
ylim

Can be a vector of length 2 applied to all coverage tracks. Alternatively, if passing a list of BigWigFlieList objects to the coverage argument, this can be a named list of numeric vectors with names matching coverage

+
annotation

Each BigWigFileList needs annotations to be passed to this argument as a named GRangesList, with names being used to @@ -368,6 +479,7 @@

Displaying Coverage Tracks

If coverage is a list, then a named list of GRangesList objects should be supplied, with each being displayed above the corresponding track from the coverage object.

+
annotcol

A vector of colours corresponding to all names within all GRangesList elements supplied as annotation. It is assumed that the @@ -375,9 +487,13 @@

Displaying Coverage Tracks

the colours should not be provided as a list which matches the coverage tracks. Instead, every named element anywhere in the annotation GRanges, across all of the tracks must be included as a colour

+
annotsize

Relative size of the tracks compared to others

+ +
+

Examples

# \donttest{
@@ -425,12 +541,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotOverlaps-methods.html b/reference/plotOverlaps-methods.html index 4b87ca0..8154bd2 100644 --- a/reference/plotOverlaps-methods.html +++ b/reference/plotOverlaps-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Plot Overlaps Between List Elements

- Source: R/AllGenerics.R, R/plotOverlaps.R + Source: R/AllGenerics.R, R/plotOverlaps.R
+

Plot Overlaps between list elements as an upset or Venn diagram

+ 
plotOverlaps(x, ...)
 
@@ -89,41 +99,67 @@ 
Plot Overlaps Between List Elements

   exp_sets = 0.25
 )
+

Arguments

-
x
+ + +
x

GRangesList of S3 list able to be coerced to character vectors

+ +
...

Passed to draw.pairwise.venn (or draw.single/triple.venn) for Venn Diagrams, and to upset for UpSet plots

+ +
type

The type of plot to be produced

+ +
var

Column to summarised as a boxplot in an upper panel (UpSet plot only)

+ +
f

Summarisation function. Must return a single value from any numeric vector

+ +
set_col

Colours to be assigned to each set

+ +
.sort_sets

passed to sort_sets in upset

+ +
hj_sets

Horizontal adjustment of set size labels

+ +
sz_sets

Text size for set size labels. Passed internally to geom_text(size = sz_sets)

+ +
exp_sets

X-axis expansion for set size panel

+ +
merge_within

Passed to makeConsensus

+ +
ignore.strand

Passed to reduce

+

Value

-

Either a VennDiagram (i.e. grid) object, or a ComplexUpset plot

+

Either a VennDiagram (i.e. grid) object, or a ComplexUpset plot

Details

@@ -138,6 +174,7 @@

Details

Values will be summarised across all elements using the requested function and the boxplot will be included as an upper panel above the intersections

+

Examples

## Examples using a list of character vectors
@@ -172,12 +209,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotPairwise.html b/reference/plotPairwise.html index 0335928..ac78aa4 100644 --- a/reference/plotPairwise.html +++ b/reference/plotPairwise.html @@ -3,6 +3,8 @@ + +
+ + +

Plot Pairwise Values from a GRangeList

- Source: R/plotPairwise.R + Source: R/plotPairwise.R
+

Plot Pairwise Values from a GRangeList by overlapping GRanges

+ 
plotPairwise(
   x,
@@ -94,75 +104,127 @@ 
Plot Pairwise Values from a GRangeList

   ...
 )
+

Arguments

-
x
+ + +
x

A GRangesList

+ +
var

The colunm to compare between list elements

+ +
colour

Optional column to use for combining across elements and setting point colour

+ +
label

Optional column to use for labelling ranges with the most extreme changes

+ +
index

Which list elements to compare

+ +
p, method, ignore.strand, min_width

Passed to makeConsensus()

+ +
xside, yside

Will call geom_(x/y)side* from the package ggside and show additional panels on the top and right of the plot respectively

+ +
side_panel_width

Set the relative widths of the side panels

+ +
side_alpha

Set fill transparency in side panels

+ +
xside_axis_pos

Position for axis_labels in the top panel when using a discrete axis

+ +
yside_axis_label

Wrapping for axis labels on the right-side panel when using a discrete axis. Set to waiver() to turn off wrapping

+ +
smooth

logical(1). If TRUE a regression line will be drawn using geom_smooth. To add this manually, set to FALSE and call this geom with any custom parameters after creating the plot

+ +
rho_geom

Used to add correlation coefficients for the two values

+ +
rho_col, rho_size, rho_alpha

Parameters for displaying the correlation

+ +
rho_pos

Place the correlation coefficient within the plotting region

+ +
label_geom

Used to add labels from the column specified in label

+ +
label_width

Label text will be truncated to this length

+ +
label_sep

If multiple values (e.g. genes) are mapped to a range, separate values using this string

+ +
label_size, label_alpha

Passed to the geom used for adding labels

+ +
min_d

Labels will only be added if the points lie circle beyond a sircle of this radius

+ +
group_sep

Text separator used to separate categories when specifying colour

+ +
simplify_equal

logical(1) When combining columns from both elements for the colour categories, should shared values be annotated as 'Both ...' instead of having longer, more difficult to read annotations.

+ +
name_sep

Character string to separate names of the GRangesList and the selected column. Will appear as axis-labels

+ +
plot_theme

Sets the initial theme by using the default theme for the current R session via get_theme()

+ +
...

Passed to geom_point() for the main panel

+

Value

-

A ggside or ggplot2 object

+

A ggside or ggplot2 object

Details

@@ -188,6 +250,7 @@

Details

A regression line and correlation co-efficient are added to the plot by default, but can be hidden easily if preferred

+

Examples

theme_set(theme_bw())
@@ -235,12 +298,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotPie-methods.html b/reference/plotPie-methods.html index 92163cf..b350f23 100644 --- a/reference/plotPie-methods.html +++ b/reference/plotPie-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Draw Pie Graphs based on one or more columns

- Source: R/AllGenerics.R, R/plotPie.R + Source: R/AllGenerics.R, R/plotPie.R
+

Draw Pie Graphs based one or more data.frame columns

+ 
plotPie(object, ...)
 
@@ -95,70 +105,108 @@ 
Draw Pie Graphs based on one or more columns

   ...
 )
+

Arguments

-
object
+ + +
object

An object (data.frame)

+ +
...

Not used

+ +
scale_by

Scale the counts by this column. In this case of a GRanges object this defaults to the count (scale_by = "n") but can also be specified as being width of each range (scale_by = "width"). If choosing width, width will be displayed in Kb

+ +
fill

The category/column used to fill the slices of the pie charts

+ +
x

The second (optional) category/column to place along the x-axis

+ +
y

The final (optional) category/column to plce along the y-axis

+ +
scale_factor

When scaling by another column, such as width, totals will be divided by this value, with 1000 being the default to provide output in kb.

+ +
width

Scale the width of all pies

+ +
total_geom

The geom_* to use for the totals at the centre of each pie. Setting this to 'none' will disable totals

+ +
total_glue

glue syntax to use for the totals in the centre of each pie. The column 'N' will produce the totals and any other values or formatting may be added here.

+ +
total_colour, total_fill, total_alpha, total_size

Colour, fill, alpha and size for the main totals in the centre of each pie chart

+ +
min_p

The minimum proportion of the total required for adding labels. Effectively removes labels from pie charts with few members. Alternatively when only one column is specified, categories below this will not be shown around the edge of the plot

+ +
max_p

only display labels for segments representing less than this proportion of the total.

+ +
cat_geom

The geom_* to use for category labels corresponding to each slice of the pie. Setting this to 'none' will disable category labels

+ +
cat_glue

glue syntax to use for the category labels corresponding to each slice of the pie charts. The columns 'n' and 'p' can be used to print totals and proportions for each slice.

+ +
cat_colour, cat_fill, cat_size, cat_alpha

Colour, fill, size and alpha for category labels

+ +
cat_adj

Adjust category labels

+ +
hole_width

Add a hole in the middle to turn the plot into a donut. Values between zero and 1 work best. Only implemented for pie charts using one value (i.e. fill)

+

Value

-

A ggplot2 object able to be customised with colour scales and themes.

+

A ggplot2 object able to be customised with colour scales and themes.

Also note that the $data element of the returned object will contain the -data.frame used for plotting. The additional column label_radians

-

represents the mid-point of each pie slice and can be used for manually +data.frame used for plotting. The additional column label_radians +represents the mid-point of each pie slice and can be used for manually adding labels to each pie. Only applies when plotting across the x or y axes

@@ -178,6 +226,7 @@

Details

in the centre using geom_label. Parameters for these labels are customisable

+

Examples

set.seed(200)
@@ -228,12 +277,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotProfileHeatmap-methods.html b/reference/plotProfileHeatmap-methods.html index da4452d..07ad1c9 100644 --- a/reference/plotProfileHeatmap-methods.html +++ b/reference/plotProfileHeatmap-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Draw a coverage Profile Heatmap

- Source: R/plotProfileHeatmap.R + Source: R/plotProfileHeatmap.R
+

Plot a coverage Profile Heatmap across multiple ranges

+ 
plotProfileHeatmap(object, ...)
 
@@ -105,37 +115,62 @@ 
Draw a coverage Profile Heatmap

   ...
 )
+

Arguments

-
object
+ + +
object

A GRanges or GRangesList object

+ +
...

Passed to facet_grid internally. Can be utilised for switching panel strips or passing a labeller function

+ +
profileCol

Column name specifying where to find the profile DataFrames

+ +
xValue, fillValue

Columns within the profile DataFrames for heatmaps

+ +
facetX, facetY

Columns used for faceting across the x- or y-axis respectively

+ +
colour

Column used for colouring lines in the summary panel. Defaults to any column used for facetY

+ +
linetype

Column used for linetypes in the summary panel

+ +
summariseBy

Function for creating the summary plot in the top panel. If set to 'none', no summary plot will be drawn. Otherwise the top panel will contain a line-plot representing this summary value for each x-axis bin

+ +
xLab, yLab, fillLab

Labels for plotting aesthetics. Can be overwritten using labs() on any returned object

+ +
labelFunX

Function for formatting x-axis labels

+ +
relHeight

The relative height of the top summary panel. Represents the fraction of the plotting area taken up by the summary panel.

+ +
sortFilter

If calling on a GRangesList, a method for subsetting the original object (e.g. 1:2). If calling on a GRanges object should be and @@ -144,20 +179,27 @@

Arguments

the heatmap such that ranges can be sorted by one or specific samples, or all. Ranges will always be sorted such that those with the strongest signal are at the top of the plot

+ +
maxDist

Maximum distance from the centre to find the strongest signal when arranging the ranges

+ +
summaryLabelSide

Side to place y-axis for the summary plot in the top panel

+ +
respectLevels

logical(1) If FALSE, facets along the y-axis will be arranged in descending order of signal, otherwise any original factor levels will be retained

+

Value

-

A ggplot2 object, able to be customised using standard ggplot2 syntax

+

A ggplot2 object, able to be customised using standard ggplot2 syntax

Details

@@ -182,6 +224,7 @@

Details

original element names as the column "name" which can be seen in the $data element of any resultant ggplot object produced by this function.

+

Examples

# \donttest{
@@ -212,12 +255,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/plotSplitDonut-methods.html b/reference/plotSplitDonut-methods.html index 87ecdd3..73bb515 100644 --- a/reference/plotSplitDonut-methods.html +++ b/reference/plotSplitDonut-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Draw Two-Level Donut Charts

- Source: R/AllGenerics.R, R/plotSplitDonut.R + Source: R/AllGenerics.R, R/plotSplitDonut.R
+

Create Donut charts based on one or two columns in a data frame

+ 
plotSplitDonut(object, ...)
 
@@ -123,102 +133,166 @@ 
Draw Two-Level Donut Charts

   ...
 )
+

Arguments

-
object
+ + +
object

A GRanges or data.frame-like object

+ +
...

Not used

+ +
scale_by

Column to scale values by. If provided, values in this column will be summed, instead of simply counting entries. Any label in the centre of the plot will also reflect this difference

+ +
inner

Column name to create the inner ring

+ +
outer

Column name to create the outer ring, subset by the inner ring

+ +
scale_factor

When scaling by another column, such as width, totals will be divided by this value, with 1000 being the default to provide output in kb.

+ +
r_centre

The radius of the hole in the centre. Setting to zero will create a Pie chart

+ +
r_inner, r_outer

The radii of the inner/outer rings

+ +
total_glue

glue-syntax for formatting the total which appears in the centre of the plot. Internally, the value N will be calculated and as such, this value should appear within this argument.

+ +
total_size

Label size total number of entries in the centre of the plot.

+ +
total_colour

Label colour for the summary total in the centre

+ +
inner_glue, outer_glue

glue-syntax for formatting labels which appear on each inner/outer segment Internally, the values n and p will be calculated as totals and proportions of the total. As such, these values can appear within this argument, as well as the fields described in the details

+ +
total_label, inner_label, outer_label

Can take values 'text', 'label' or 'none'. If setting one the first two values, the labelling function geom_* will be called, otherwise no label will be drawn

+ +
label_alpha, inner_label_alpha, outer_label_alpha

transparency for labels

+ +
label_size, inner_label_size, outer_label_size

Size of all text labels

+ +
label_colour, inner_label_colour, outer_label_colour

Takes any colour specification, with the additional option of 'palette'. In this special case, the same palette as is used for each segment will be applied.

+ +
min_p, inner_min_p, outer_min_p

only display labels for segments representing greater than this proportion of the total. If inner/outer values are specified, the values in min_p will be ignored for that layer

+ +
max_p, inner_max_p, outer_max_p

only display labels for segments representing less than this proportion of the total. If inner/outer values are specified, the values in max_p will be ignored for that layer

+ +
inner_pattern, outer_pattern

Regular expressions which are combined with max_p and min_p values for accurately choosing labels

+ +
inner_rotate, outer_rotate

logical(1). Rotate labels for inner or outer rings. This will be ignored by when setting the geom as "label". See geom_text

+ +
explode_inner, explode_outer

Regular expressions from either the inner or outer ring for which segments will be 'exploded'

+ +
explode_query

Setting to AND and specifying values for both the inner and outer ring will require matches in both categories

+ +
explode_x, explode_y

Numeric values for shifting exploded values

+ +
explode_r

Radius expansion for exploded values

+ +
nudge_r, inner_nudge_r, outer_nudge_r

Radius expansion for labels

+ +
expand

Passed to expansion for both x and y axes. Can be helpful if labels are clipped by plot limits

+ +
inner_palette

Colour palette for the inner ring

+ +
outer_palette

Optional colour palette for the outer ring

+ +
inner_legend, outer_legend

logical(1). Show legends for either layer

+ +
outer_p_by

Scale the proportions for outer segments by the complete dataset, or within each inner segment

+ +
layout

Passed to plot_layout

+

Value

-

A patchwork object consisting of both ggplot2 objects and legend grobs

+

A patchwork object consisting of both ggplot2 objects and legend grobs

Details

@@ -250,6 +324,7 @@

Details

labels using this strategy enabling a wide variety of labelling approaches to be utilised.

+

Examples

set.seed(200)
@@ -283,12 +358,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/propOverlap-methods.html b/reference/propOverlap-methods.html index 26a74f3..1b5011c 100644 --- a/reference/propOverlap-methods.html +++ b/reference/propOverlap-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Find the proportions of an overlapping range

- Source: R/AllGenerics.R, R/propOverlaps.R + Source: R/AllGenerics.R, R/propOverlaps.R
+

Find the proportion of a query reange which overlaps the subject

+ 
propOverlap(x, y, ...)
 
 # S4 method for class 'GRanges,GRanges'
 propOverlap(x, y, ignore.strand = FALSE, ...)
+

Arguments

-
x, y
+ + +
x, y

A GenomicRanges object

+ +
...

Not used

+ +
ignore.strand

If set to TRUE, then the strand of x and y is set to "*" prior to any computation.

+

Value

-

Numeric vector the same length as x

+

Numeric vector the same length as x

Details

@@ -84,6 +102,7 @@

Details

of the query range which overlaps one or more subject ranges is returned instead of a logical vector

+

Examples

x <- GRanges("chr1:1-10")
@@ -100,12 +119,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/reduceMC.html b/reference/reduceMC.html index 7597483..374cf75 100644 --- a/reference/reduceMC.html +++ b/reference/reduceMC.html @@ -3,6 +3,8 @@ + +
+ + +

Reduce ranges retaining mcols

- Source: R/reduceMC.R + Source: R/reduceMC.R
+

Reduce ranges retaining mcols

+ 
reduceMC(x, ignore.strand = FALSE, simplify = TRUE, ...)
+

Arguments

-
x
+ + +
x

A GenomicRanges object

+ +
ignore.strand

If set to TRUE, then the strand of x and y is set to "*" prior to any computation.

+ +
simplify

logical(1). Attempt to simplify returned columns where possible

+ +
...

Passed to reduce

+

Value

-

A GRanges object

+

A GRanges object

Details

@@ -86,6 +106,7 @@

Details

mcols will be returned as CompressedList columns.

If simplify = TRUE columns will be returned as vectors where possible.

+

Examples

x <- GRanges(c("chr1:1-10:+", "chr1:6-12:-"))
@@ -113,12 +134,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/setoptsMC-methods.html b/reference/setoptsMC-methods.html index 1565165..966aeb2 100644 --- a/reference/setoptsMC-methods.html +++ b/reference/setoptsMC-methods.html @@ -3,6 +3,8 @@ + +
+ + +

Perform set operations retaining mcols

- Source: R/AllGenerics.R, R/setoptsMC.R + Source: R/AllGenerics.R, R/setoptsMC.R
+

Perform set operations retaining all mcols from the query range

+ 
setdiffMC(x, y, ...)
 
@@ -74,23 +84,33 @@ 
Perform set operations retaining mcols

 # S4 method for class 'GRanges,GRanges'
 unionMC(x, y, ignore.strand = FALSE, simplify = TRUE, ...)
+

Arguments

-
x, y
+ + +
x, y

GenomicRanges objects

+ +
...

Not used

+ +
ignore.strand

If set to TRUE, then the strand of x and y is set to "*" prior to any computation.

+ +
simplify

logical(1) If TRUE, any List columns will be returned as vectors where possible. This can only occur if single, unique entries are present in all initial elements.

+

Value

-

A GRanges object with all mcols returned form the original object. +

A GRanges object with all mcols returned form the original object. If a range obtained by setdiff maps back to two or more ranges in the original set of Ranges, mcols will be returned as CompressedList columns

@@ -111,6 +131,7 @@

Details

further modified by many functions included in the plyranges package, such as mutate().

+

Examples

x <- GRanges("chr1:1-100:+")
@@ -168,12 +189,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/stitchRanges.html b/reference/stitchRanges.html index 4d5b404..a6402a5 100644 --- a/reference/stitchRanges.html +++ b/reference/stitchRanges.html @@ -4,6 +4,8 @@ + +
+ + +

Stitch Ranges within a given distance

- Source: R/stitchRanges.R + Source: R/stitchRanges.R
+

Stitch together ranges within a given distance, using excluded ranges as barriers that cannot be crossed

+ 
stitchRanges(x, exclude, maxgap = 12500L, ignore.strand = TRUE)
+

Arguments

-
x
+ + +
x

Ranges to be stitched together

+ +
exclude

Ranges to exclude

+ +
maxgap

The maximum distance between ranges to be stitched

+ +
ignore.strand

logical

+

Value

-

A GRanges object

+

A GRanges object

Details

@@ -85,6 +105,7 @@

Details

useful if wanting to stitch enhancers whilst excluding promoters.

All inputs and outputs are Genomic Ranges objects

+

Examples

x <- GRanges(c("chr1:1-10", "chr1:101-110", "chr1:201-210", "chr2:1-10"))
@@ -106,12 +127,22 @@ 
Examples
+ +
+ + + + + + diff --git a/reference/voomWeightsFromCPM.html b/reference/voomWeightsFromCPM.html index f53b8e1..e851437 100644 --- a/reference/voomWeightsFromCPM.html +++ b/reference/voomWeightsFromCPM.html @@ -3,6 +3,8 @@ + +
+ + +

Estimate voom precision weights directly From CPM values

- Source: R/voomWeightsFromCPM.R + Source: R/voomWeightsFromCPM.R
+

Estimate voom precision weights directly From CPM values

+ 
voomWeightsFromCPM(
   cpm,
@@ -69,30 +79,46 @@ 
Estimate voom precision weights directly From CPM values

   ...
 )
+

Arguments

-
cpm
+ + +
cpm

Matrix of CPM or logCPM values

+ +
design

The design matrix for the experiment

+ +
w0

Initial vector of sample weights. Should be calculated using arrayWeights

+ +
lib.size

Initial library sizes. Must be provided as these are no estimable from CPM values

+ +
isLogCPM

logical(1). Indicates whether the data is log2 transformed already. Most commonly (e.g. if using the output of cqn) it will be,

+ +
span

Width of the smoothing window used for the lowess mean-variance trend. Expressed as a proportion between 0 and 1.

+ +
...

Passed to lmFit internally

+

Value

-

An object of class EList as would be output by voom. +

An object of class EList as would be output by voom. Importantly, there will be no genes element, although this can be added later. Similarly, the returned targets element will only contain sample @@ -102,8 +128,8 @@

Value

been offset by the library sizes and will be simple logCPM values. As such, the fitted Amean is also returned in this list element.

If initial sample weights were provided, modified weights will also be -returned, as the initial function voomWithQualityWeights

-

performs two rounds of estimation of sample weights. +returned, as the initial function voomWithQualityWeights +performs two rounds of estimation of sample weights. Here we would simply provide the initial weights a priori, with the second round performed within the function. Importantly, this second round of sample weight estimation uses the precision @@ -132,6 +158,7 @@

Details

relationship, whilst the second round is after incorporation of the precision weights.

+

Examples

bamFiles <- system.file("exdata", c("rep1.bam", "rep2.bam"), package="csaw")
@@ -146,12 +173,22 @@ 
Examples
+ +
+ + + + + + diff --git a/sitemap.xml b/sitemap.xml index 8af3636..72847e2 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -1,165 +1,57 @@ - - - - /404.html - - - /articles/differential_signal_fixed.html - - - /articles/differential_signal_sliding.html - - - /articles/index.html - - - /articles/range_based_functions.html - - - /authors.html - - - /index.html - - - /news/index.html - - - /reference/addDiffStatus-methods.html - - - /reference/as_tibble.html - - - /reference/bestOverlap-methods.html - - - /reference/chopMC.html - - - /reference/colToRanges-methods.html - - - /reference/collapseGenes.html - - - /reference/cytobands.html - - - /reference/defineRegions.html - - - /reference/defineSeqinfo.html - - - /reference/distinctMC.html - - - /reference/dot-makeFinalProfileHeatmap.html - - - /reference/dot-mapFeatures.html - - - /reference/dot-mapGi.html - - - /reference/dot-mapWithin.html - - - /reference/dualFilter.html - - - /reference/ex_datasets.html - - - /reference/extraChIPs-package.html - - - /reference/fitAssayDiff-methods.html - - - /reference/fixed_width_datasets.html - - - /reference/getProfileData-methods.html - - - /reference/grlToSE-methods.html - - - /reference/importPeaks.html - - - /reference/index.html - - - /reference/makeConsensus.html - - - /reference/mapByFeature.html - - - /reference/mapGrlCols.html - - - /reference/mergeByCol-methods.html - - - /reference/mergeByHMP-methods.html - - - /reference/mergeBySig-methods.html - - - /reference/partitionRanges-methods.html - - - /reference/plotAssayDensities-methods.html - - - /reference/plotAssayHeatmap-methods.html - - - /reference/plotAssayPCA-methods.html - - - /reference/plotAssayRle-methods.html - - - /reference/plotGrlCol.html - - - /reference/plotHFGC.html - - - /reference/plotOverlaps-methods.html - - - /reference/plotPairwise.html - - - /reference/plotPie-methods.html - - - /reference/plotProfileHeatmap-methods.html - - - /reference/plotSplitDonut-methods.html - - - /reference/propOverlap-methods.html - - - /reference/reduceMC.html - - - /reference/setoptsMC-methods.html - - - /reference/stitchRanges.html - - - /reference/voomWeightsFromCPM.html - + +/404.html +/articles/differential_signal_fixed.html +/articles/differential_signal_sliding.html +/articles/index.html +/articles/range_based_functions.html +/authors.html +/index.html +/news/index.html +/reference/addDiffStatus-methods.html +/reference/as_tibble.html +/reference/bestOverlap-methods.html +/reference/chopMC.html +/reference/colToRanges-methods.html +/reference/collapseGenes.html +/reference/cytobands.html +/reference/defineRegions.html +/reference/defineSeqinfo.html +/reference/distinctMC.html +/reference/dot-makeFinalProfileHeatmap.html +/reference/dot-mapFeatures.html +/reference/dot-mapGi.html +/reference/dot-mapWithin.html +/reference/dualFilter.html +/reference/ex_datasets.html +/reference/extraChIPs-package.html +/reference/fitAssayDiff-methods.html +/reference/fixed_width_datasets.html +/reference/getProfileData-methods.html +/reference/grlToSE-methods.html +/reference/importPeaks.html +/reference/index.html +/reference/makeConsensus.html +/reference/mapByFeature.html +/reference/mapGrlCols.html +/reference/mergeByCol-methods.html +/reference/mergeByHMP-methods.html +/reference/mergeBySig-methods.html +/reference/partitionRanges-methods.html +/reference/plotAssayDensities-methods.html +/reference/plotAssayHeatmap-methods.html +/reference/plotAssayPCA-methods.html +/reference/plotAssayRle-methods.html +/reference/plotGrlCol.html +/reference/plotHFGC.html +/reference/plotOverlaps-methods.html +/reference/plotPairwise.html +/reference/plotPie-methods.html +/reference/plotProfileHeatmap-methods.html +/reference/plotSplitDonut-methods.html +/reference/propOverlap-methods.html +/reference/reduceMC.html +/reference/setoptsMC-methods.html +/reference/stitchRanges.html +/reference/voomWeightsFromCPM.html +