From 1f840241d50e533f2e7c3cf3177c8ffaf6464fd2 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sun, 7 Apr 2024 03:10:28 +0000 Subject: [PATCH] cli-14590-952 --- 404.html | 2 +- articles/differential_signal_fixed.html | 75 +++++++------- articles/differential_signal_sliding.html | 73 ++++++------- articles/index.html | 2 +- articles/range_based_functions.html | 113 +++++++++++---------- authors.html | 6 +- index.html | 2 +- news/index.html | 10 +- pkgdown.yml | 2 +- reference/addDiffStatus-methods.html | 2 +- reference/as_tibble.html | 2 +- reference/bestOverlap-methods.html | 2 +- reference/chopMC.html | 2 +- reference/colToRanges-methods.html | 2 +- reference/collapseGenes.html | 2 +- reference/cytobands.html | 2 +- reference/defineRegions.html | 2 +- reference/defineSeqinfo.html | 2 +- reference/distinctMC.html | 2 +- reference/dot-makeFinalProfileHeatmap.html | 2 +- reference/dot-mapFeatures.html | 2 +- reference/dot-mapGi.html | 2 +- reference/dot-mapWithin.html | 2 +- reference/dualFilter.html | 2 +- reference/ex_datasets.html | 2 +- reference/extraChIPs-package.html | 2 +- reference/fitAssayDiff-methods.html | 2 +- reference/fixed_width_datasets.html | 2 +- reference/getProfileData-methods.html | 2 +- reference/grlToSE-methods.html | 2 +- reference/importPeaks.html | 2 +- reference/index.html | 2 +- reference/makeConsensus.html | 15 ++- reference/mapByFeature.html | 2 +- reference/mapGrlCols.html | 2 +- reference/mergeByCol-methods.html | 2 +- reference/mergeByHMP-methods.html | 2 +- reference/mergeBySig-methods.html | 2 +- reference/partitionRanges-methods.html | 2 +- reference/plotAssayDensities-methods.html | 2 +- reference/plotAssayHeatmap-methods.html | 2 +- reference/plotAssayPCA-methods.html | 2 +- reference/plotAssayRle-methods.html | 2 +- reference/plotGrlCol.html | 2 +- reference/plotHFGC.html | 2 +- reference/plotOverlaps-methods.html | 10 +- reference/plotPairwise.html | 2 +- reference/plotPie-methods.html | 2 +- reference/plotProfileHeatmap-methods.html | 2 +- reference/plotSplitDonut-methods.html | 2 +- reference/propOverlap-methods.html | 2 +- reference/reduceMC.html | 2 +- reference/setoptsMC-methods.html | 2 +- reference/stitchRanges.html | 2 +- reference/voomWeightsFromCPM.html | 2 +- 55 files changed, 208 insertions(+), 190 deletions(-) diff --git a/404.html b/404.html index cb6c54d..6fbe475 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/articles/differential_signal_fixed.html b/articles/differential_signal_fixed.html index 395eb72..0c79a75 100644 --- a/articles/differential_signal_fixed.html +++ b/articles/differential_signal_fixed.html @@ -33,7 +33,7 @@ extraChIPs - 1.7.6 + 1.7.7 @@ -735,7 +735,7 @@

Session Info
 sessionInfo()
-
## R Under development (unstable) (2024-03-28 r86224)
+
## R Under development (unstable) (2024-04-03 r86327)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -762,16 +762,16 @@ 
Session Info##  [1] quantro_1.37.0              here_1.0.1                 
 ##  [3] ggrepel_0.9.5               glue_1.7.0                 
 ##  [5] scales_1.3.0                plyranges_1.23.0           
-##  [7] extraChIPs_1.7.6            ggside_0.3.1               
+##  [7] extraChIPs_1.7.7            ggside_0.3.1               
 ##  [9] patchwork_1.2.0             edgeR_4.1.19               
-## [11] limma_3.59.6                rtracklayer_1.63.1         
+## [11] limma_3.59.6                rtracklayer_1.63.2         
 ## [13] BiocParallel_1.37.1         csaw_1.37.1                
 ## [15] SummarizedExperiment_1.33.3 Biobase_2.63.1             
 ## [17] MatrixGenerics_1.15.0       matrixStats_1.2.0          
 ## [19] Rsamtools_2.19.4            Biostrings_2.71.5          
 ## [21] XVector_0.43.1              GenomicRanges_1.55.4       
-## [23] GenomeInfoDb_1.39.9         IRanges_2.37.1             
-## [25] S4Vectors_0.41.5            BiocGenerics_0.49.1        
+## [23] GenomeInfoDb_1.39.12        IRanges_2.37.1             
+## [25] S4Vectors_0.41.6            BiocGenerics_0.49.1        
 ## [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                
@@ -783,8 +783,8 @@ 
Session Info##   [1] fs_1.6.3                   ProtGenerics_1.35.4       
 ##   [3] bitops_1.0-7               httr_1.4.7                
 ##   [5] RColorBrewer_1.1-3         doParallel_1.0.17         
-##   [7] InteractionSet_1.31.0      tools_4.5.0               
-##   [9] doRNG_1.8.6                backports_1.4.1           
+##   [7] InteractionSet_1.31.0      doRNG_1.8.6               
+##   [9] tools_4.5.0                backports_1.4.1           
 ##  [11] utf8_1.2.4                 R6_2.5.1                  
 ##  [13] HDF5Array_1.31.6           mgcv_1.9-1                
 ##  [15] lazyeval_0.2.2             Gviz_1.47.1               
@@ -810,7 +810,7 @@ 
Session Info##  [55] crayon_1.5.2               lattice_0.22-6            
 ##  [57] ComplexUpset_1.3.3         GenomicFeatures_1.55.4    
 ##  [59] annotate_1.81.2            KEGGREST_1.43.0           
-##  [61] pillar_1.9.0               knitr_1.45                
+##  [61] pillar_1.9.0               knitr_1.46                
 ##  [63] beanplot_1.3.1             metapod_1.11.1            
 ##  [65] rjson_0.2.21               codetools_0.2-20          
 ##  [67] data.table_1.15.4          vctrs_0.6.5               
@@ -821,7 +821,7 @@ 
Session Info##  [77] GenomicInteractions_1.37.0 nlme_3.1-164              
 ##  [79] bit64_4.0.5                progress_1.2.3            
 ##  [81] filelock_1.0.3             rprojroot_2.0.4           
-##  [83] bslib_0.7.0                nor1mix_1.3-2             
+##  [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               
 ##  [89] nnet_7.3-19                tidyselect_1.2.1          
@@ -832,38 +832,39 @@ 
Session Info##  [99] bookdown_0.38              checkmate_2.3.1           
 ## [101] quadprog_1.5-8             rappdirs_0.3.3            
 ## [103] digest_0.6.35              rmarkdown_2.26            
-## [105] GEOquery_2.71.0            htmltools_0.5.8           
+## [105] GEOquery_2.71.0            htmltools_0.5.8.1         
 ## [107] pkgconfig_2.0.3            jpeg_0.1-10               
 ## [109] base64enc_0.1-3            sparseMatrixStats_1.15.0  
 ## [111] highr_0.10                 dbplyr_2.5.0              
 ## [113] fastmap_1.1.1              ensembldb_2.27.1          
 ## [115] rlang_1.1.3                htmlwidgets_1.6.4         
-## [117] DelayedMatrixStats_1.25.1  farver_2.1.1              
-## [119] jquerylib_0.1.4            jsonlite_1.8.8            
-## [121] mclust_6.1                 VariantAnnotation_1.49.7  
-## [123] RCurl_1.98-1.14            magrittr_2.0.3            
-## [125] Formula_1.2-5              GenomeInfoDbData_1.2.12   
-## [127] Rhdf5lib_1.25.1            munsell_0.5.1             
-## [129] Rcpp_1.0.12                stringi_1.8.3             
-## [131] zlibbioc_1.49.3            MASS_7.3-60.2             
-## [133] plyr_1.8.9                 bumphunter_1.45.1         
-## [135] minfi_1.49.1               parallel_4.5.0            
-## [137] deldir_2.0-4               splines_4.5.0             
-## [139] multtest_2.59.0            hms_1.1.3                 
-## [141] locfit_1.5-9.9             igraph_2.0.3              
-## [143] rngtools_1.5.2             biomaRt_2.59.1            
-## [145] futile.options_1.0.1       XML_3.99-0.16.1           
-## [147] evaluate_0.23              latticeExtra_0.6-30       
-## [149] biovizBase_1.51.0          lambda.r_1.2.4            
-## [151] BiocManager_1.30.22        tzdb_0.4.0                
-## [153] foreach_1.5.2              tweenr_2.0.3              
-## [155] openssl_2.1.1              polyclip_1.10-6           
-## [157] reshape_0.8.9              ggforce_0.4.2             
-## [159] broom_1.0.5                xtable_1.8-4              
-## [161] restfulr_0.0.15            AnnotationFilter_1.27.0   
-## [163] ragg_1.3.0                 memoise_2.0.1             
-## [165] AnnotationDbi_1.65.2       GenomicAlignments_1.39.5  
-## [167] cluster_2.1.6              timechange_0.3.0

+## [117] UCSC.utils_0.99.5          DelayedMatrixStats_1.25.1 
+## [119] farver_2.1.1               jquerylib_0.1.4           
+## [121] jsonlite_1.8.8             mclust_6.1                
+## [123] VariantAnnotation_1.49.7   RCurl_1.98-1.14           
+## [125] magrittr_2.0.3             Formula_1.2-5             
+## [127] GenomeInfoDbData_1.2.12    Rhdf5lib_1.25.3           
+## [129] munsell_0.5.1              Rcpp_1.0.12               
+## [131] stringi_1.8.3              zlibbioc_1.49.3           
+## [133] MASS_7.3-60.2              plyr_1.8.9                
+## [135] bumphunter_1.45.1          minfi_1.49.1              
+## [137] parallel_4.5.0             deldir_2.0-4              
+## [139] splines_4.5.0              multtest_2.59.0           
+## [141] hms_1.1.3                  locfit_1.5-9.9            
+## [143] igraph_2.0.3               rngtools_1.5.2            
+## [145] biomaRt_2.59.1             futile.options_1.0.1      
+## [147] XML_3.99-0.16.1            evaluate_0.23             
+## [149] latticeExtra_0.6-30        biovizBase_1.51.0         
+## [151] lambda.r_1.2.4             BiocManager_1.30.22       
+## [153] tzdb_0.4.0                 foreach_1.5.2             
+## [155] tweenr_2.0.3               openssl_2.1.1             
+## [157] polyclip_1.10-6            reshape_0.8.9             
+## [159] ggforce_0.4.2              broom_1.0.5               
+## [161] xtable_1.8-4               restfulr_0.0.15           
+## [163] AnnotationFilter_1.27.0    ragg_1.3.0                
+## [165] memoise_2.0.1              AnnotationDbi_1.65.2      
+## [167] GenomicAlignments_1.39.5   cluster_2.1.6             
+## [169] timechange_0.3.0

References diff --git a/articles/differential_signal_sliding.html b/articles/differential_signal_sliding.html index 6f4ce60..0537ece 100644 --- a/articles/differential_signal_sliding.html +++ b/articles/differential_signal_sliding.html @@ -33,7 +33,7 @@ extraChIPs - 1.7.6 + 1.7.7

@@ -1270,7 +1270,7 @@

Session Info
 sessionInfo()
-
## R Under development (unstable) (2024-03-28 r86224)
+
## R Under development (unstable) (2024-04-03 r86327)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -1296,20 +1296,20 @@ 
Session Info## other attached packages:
 ##  [1] ggrepel_0.9.5               cqn_1.49.0                 
 ##  [3] quantreg_5.97               SparseM_1.81               
-##  [5] preprocessCore_1.65.0       nor1mix_1.3-2              
+##  [5] preprocessCore_1.65.0       nor1mix_1.3-3              
 ##  [7] mclust_6.1                  quantro_1.37.0             
 ##  [9] magrittr_2.0.3              here_1.0.1                 
 ## [11] glue_1.7.0                  scales_1.3.0               
-## [13] plyranges_1.23.0            extraChIPs_1.7.6           
+## [13] plyranges_1.23.0            extraChIPs_1.7.7           
 ## [15] ggside_0.3.1                patchwork_1.2.0            
 ## [17] edgeR_4.1.19                limma_3.59.6               
-## [19] rtracklayer_1.63.1          BiocParallel_1.37.1        
+## [19] rtracklayer_1.63.2          BiocParallel_1.37.1        
 ## [21] csaw_1.37.1                 SummarizedExperiment_1.33.3
 ## [23] Biobase_2.63.1              MatrixGenerics_1.15.0      
 ## [25] matrixStats_1.2.0           Rsamtools_2.19.4           
 ## [27] Biostrings_2.71.5           XVector_0.43.1             
-## [29] GenomicRanges_1.55.4        GenomeInfoDb_1.39.9        
-## [31] IRanges_2.37.1              S4Vectors_0.41.5           
+## [29] GenomicRanges_1.55.4        GenomeInfoDb_1.39.12       
+## [31] IRanges_2.37.1              S4Vectors_0.41.6           
 ## [33] BiocGenerics_0.49.1         lubridate_1.9.3            
 ## [35] forcats_1.0.0               stringr_1.5.1              
 ## [37] dplyr_1.1.4                 purrr_1.0.2                
@@ -1321,8 +1321,8 @@ 
Session Info##   [1] fs_1.6.3                   ProtGenerics_1.35.4       
 ##   [3] bitops_1.0-7               httr_1.4.7                
 ##   [5] RColorBrewer_1.1-3         doParallel_1.0.17         
-##   [7] InteractionSet_1.31.0      tools_4.5.0               
-##   [9] doRNG_1.8.6                backports_1.4.1           
+##   [7] InteractionSet_1.31.0      doRNG_1.8.6               
+##   [9] tools_4.5.0                backports_1.4.1           
 ##  [11] utf8_1.2.4                 R6_2.5.1                  
 ##  [13] HDF5Array_1.31.6           lazyeval_0.2.2            
 ##  [15] Gviz_1.47.1                rhdf5filters_1.15.4       
@@ -1347,7 +1347,7 @@ 
Session Info##  [53] lattice_0.22-6             ComplexUpset_1.3.3        
 ##  [55] GenomicFeatures_1.55.4     annotate_1.81.2           
 ##  [57] KEGGREST_1.43.0            pillar_1.9.0              
-##  [59] knitr_1.45                 beanplot_1.3.1            
+##  [59] knitr_1.46                 beanplot_1.3.1            
 ##  [61] metapod_1.11.1             rjson_0.2.21              
 ##  [63] codetools_0.2-20           data.table_1.15.4         
 ##  [65] vctrs_0.6.5                png_0.1-8                 
@@ -1368,37 +1368,38 @@ 
Session Info##  [95] bookdown_0.38              checkmate_2.3.1           
 ##  [97] quadprog_1.5-8             rappdirs_0.3.3            
 ##  [99] digest_0.6.35              rmarkdown_2.26            
-## [101] GEOquery_2.71.0            htmltools_0.5.8           
+## [101] GEOquery_2.71.0            htmltools_0.5.8.1         
 ## [103] pkgconfig_2.0.3            jpeg_0.1-10               
 ## [105] base64enc_0.1-3            sparseMatrixStats_1.15.0  
 ## [107] highr_0.10                 dbplyr_2.5.0              
 ## [109] fastmap_1.1.1              ensembldb_2.27.1          
 ## [111] rlang_1.1.3                htmlwidgets_1.6.4         
-## [113] DelayedMatrixStats_1.25.1  farver_2.1.1              
-## [115] jquerylib_0.1.4            jsonlite_1.8.8            
-## [117] VariantAnnotation_1.49.7   RCurl_1.98-1.14           
-## [119] Formula_1.2-5              GenomeInfoDbData_1.2.12   
-## [121] Rhdf5lib_1.25.1            munsell_0.5.1             
-## [123] Rcpp_1.0.12                stringi_1.8.3             
-## [125] zlibbioc_1.49.3            MASS_7.3-60.2             
-## [127] plyr_1.8.9                 bumphunter_1.45.1         
-## [129] minfi_1.49.1               parallel_4.5.0            
-## [131] deldir_2.0-4               multtest_2.59.0           
-## [133] hms_1.1.3                  locfit_1.5-9.9            
-## [135] igraph_2.0.3               rngtools_1.5.2            
-## [137] biomaRt_2.59.1             futile.options_1.0.1      
-## [139] XML_3.99-0.16.1            evaluate_0.23             
-## [141] latticeExtra_0.6-30        biovizBase_1.51.0         
-## [143] lambda.r_1.2.4             BiocManager_1.30.22       
-## [145] tzdb_0.4.0                 foreach_1.5.2             
-## [147] tweenr_2.0.3               MatrixModels_0.5-3        
-## [149] openssl_2.1.1              polyclip_1.10-6           
-## [151] reshape_0.8.9              ggforce_0.4.2             
-## [153] broom_1.0.5                xtable_1.8-4              
-## [155] restfulr_0.0.15            AnnotationFilter_1.27.0   
-## [157] ragg_1.3.0                 memoise_2.0.1             
-## [159] AnnotationDbi_1.65.2       GenomicAlignments_1.39.5  
-## [161] cluster_2.1.6              timechange_0.3.0

+## [113] UCSC.utils_0.99.5          DelayedMatrixStats_1.25.1 
+## [115] farver_2.1.1               jquerylib_0.1.4           
+## [117] jsonlite_1.8.8             VariantAnnotation_1.49.7  
+## [119] RCurl_1.98-1.14            Formula_1.2-5             
+## [121] GenomeInfoDbData_1.2.12    Rhdf5lib_1.25.3           
+## [123] munsell_0.5.1              Rcpp_1.0.12               
+## [125] stringi_1.8.3              zlibbioc_1.49.3           
+## [127] MASS_7.3-60.2              plyr_1.8.9                
+## [129] bumphunter_1.45.1          minfi_1.49.1              
+## [131] parallel_4.5.0             deldir_2.0-4              
+## [133] multtest_2.59.0            hms_1.1.3                 
+## [135] locfit_1.5-9.9             igraph_2.0.3              
+## [137] rngtools_1.5.2             biomaRt_2.59.1            
+## [139] futile.options_1.0.1       XML_3.99-0.16.1           
+## [141] evaluate_0.23              latticeExtra_0.6-30       
+## [143] biovizBase_1.51.0          lambda.r_1.2.4            
+## [145] BiocManager_1.30.22        tzdb_0.4.0                
+## [147] foreach_1.5.2              tweenr_2.0.3              
+## [149] MatrixModels_0.5-3         openssl_2.1.1             
+## [151] polyclip_1.10-6            reshape_0.8.9             
+## [153] ggforce_0.4.2              broom_1.0.5               
+## [155] xtable_1.8-4               restfulr_0.0.15           
+## [157] AnnotationFilter_1.27.0    ragg_1.3.0                
+## [159] memoise_2.0.1              AnnotationDbi_1.65.2      
+## [161] GenomicAlignments_1.39.5   cluster_2.1.6             
+## [163] timechange_0.3.0

References diff --git a/articles/index.html b/articles/index.html index 68d19f3..6ffef78 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7

diff --git a/articles/range_based_functions.html b/articles/range_based_functions.html index 92b6515..54a705c 100644 --- a/articles/range_based_functions.html +++ b/articles/range_based_functions.html @@ -33,7 +33,7 @@ extraChIPs - 1.7.6 + 1.7.7 @@ -642,7 +642,7 @@

Session Info
 sessionInfo()
-
## R Under development (unstable) (2024-03-28 r86224)
+
## R Under development (unstable) (2024-04-03 r86327)
 ## Platform: x86_64-pc-linux-gnu
 ## Running under: Ubuntu 22.04.4 LTS
 ## 
@@ -666,12 +666,12 @@ 
Session Info## [8] base     
 ## 
 ## other attached packages:
-##  [1] plyranges_1.23.0            extraChIPs_1.7.6           
+##  [1] plyranges_1.23.0            extraChIPs_1.7.7           
 ##  [3] SummarizedExperiment_1.33.3 Biobase_2.63.1             
 ##  [5] MatrixGenerics_1.15.0       matrixStats_1.2.0          
 ##  [7] ggside_0.3.1                GenomicRanges_1.55.4       
-##  [9] GenomeInfoDb_1.39.9         IRanges_2.37.1             
-## [11] S4Vectors_0.41.5            BiocGenerics_0.49.1        
+##  [9] GenomeInfoDb_1.39.12        IRanges_2.37.1             
+## [11] S4Vectors_0.41.6            BiocGenerics_0.49.1        
 ## [13] BiocParallel_1.37.1         lubridate_1.9.3            
 ## [15] forcats_1.0.0               stringr_1.5.1              
 ## [17] dplyr_1.1.4                 purrr_1.0.2                
@@ -699,58 +699,59 @@ 
Session Info##  [33] rappdirs_0.3.3             GenomeInfoDbData_1.2.12   
 ##  [35] ggrepel_0.9.5              pkgdown_2.0.7.9000        
 ##  [37] codetools_0.2-20           DelayedArray_0.29.9       
-##  [39] xml2_1.3.6                 ggforce_0.4.2             
+##  [39] ggforce_0.4.2              xml2_1.3.6                
 ##  [41] tidyselect_1.2.1           futile.logger_1.4.3       
-##  [43] farver_2.1.1               ComplexUpset_1.3.3        
-##  [45] BiocFileCache_2.11.2       base64enc_0.1-3           
-##  [47] GenomicAlignments_1.39.5   jsonlite_1.8.8            
-##  [49] Formula_1.2-5              systemfonts_1.0.6         
-##  [51] tools_4.5.0                progress_1.2.3            
-##  [53] ragg_1.3.0                 Rcpp_1.0.12               
-##  [55] glue_1.7.0                 gridExtra_2.3             
-##  [57] SparseArray_1.3.4          xfun_0.43                 
-##  [59] withr_3.0.0                formatR_1.14              
-##  [61] BiocManager_1.30.22        fastmap_1.1.1             
-##  [63] latticeExtra_0.6-30        fansi_1.0.6               
-##  [65] digest_0.6.35              timechange_0.3.0          
-##  [67] R6_2.5.1                   textshaping_0.3.7         
-##  [69] colorspace_2.1-0           jpeg_0.1-10               
-##  [71] dichromat_2.0-0.1          biomaRt_2.59.1            
-##  [73] RSQLite_2.3.6              utf8_1.2.4                
-##  [75] generics_0.1.3             data.table_1.15.4         
-##  [77] rtracklayer_1.63.1         prettyunits_1.2.0         
-##  [79] InteractionSet_1.31.0      httr_1.4.7                
-##  [81] htmlwidgets_1.6.4          S4Arrays_1.3.6            
-##  [83] pkgconfig_2.0.3            gtable_0.3.4              
-##  [85] blob_1.2.4                 XVector_0.43.1            
-##  [87] htmltools_0.5.8            bookdown_0.38             
-##  [89] ProtGenerics_1.35.4        scales_1.3.0              
-##  [91] png_0.1-8                  knitr_1.45                
-##  [93] lambda.r_1.2.4             rstudioapi_0.16.0         
-##  [95] tzdb_0.4.0                 rjson_0.2.21              
-##  [97] checkmate_2.3.1            curl_5.2.1                
-##  [99] cachem_1.0.8               parallel_4.5.0            
-## [101] foreign_0.8-86             AnnotationDbi_1.65.2      
-## [103] restfulr_0.0.15            desc_1.4.3                
-## [105] pillar_1.9.0               grid_4.5.0                
-## [107] vctrs_0.6.5                dbplyr_2.5.0              
-## [109] cluster_2.1.6              htmlTable_2.4.2           
-## [111] evaluate_0.23              VennDiagram_1.7.3         
-## [113] GenomicFeatures_1.55.4     cli_3.6.2                 
-## [115] locfit_1.5-9.9             compiler_4.5.0            
-## [117] futile.options_1.0.1       Rsamtools_2.19.4          
-## [119] rlang_1.1.3                crayon_1.5.2              
-## [121] interp_1.1-6               fs_1.6.3                  
-## [123] stringi_1.8.3              deldir_2.0-4              
-## [125] munsell_0.5.1              Biostrings_2.71.5         
-## [127] lazyeval_0.2.2             csaw_1.37.1               
-## [129] Matrix_1.7-0               BSgenome_1.71.4           
-## [131] hms_1.1.3                  patchwork_1.2.0           
-## [133] bit64_4.0.5                KEGGREST_1.43.0           
-## [135] statmod_1.5.0              highr_0.10                
-## [137] igraph_2.0.3               broom_1.0.5               
-## [139] memoise_2.0.1              bslib_0.7.0               
-## [141] bit_4.0.5                  GenomicInteractions_1.37.0

+##  [43] farver_2.1.1               UCSC.utils_0.99.5         
+##  [45] ComplexUpset_1.3.3         BiocFileCache_2.11.2      
+##  [47] base64enc_0.1-3            GenomicAlignments_1.39.5  
+##  [49] jsonlite_1.8.8             Formula_1.2-5             
+##  [51] systemfonts_1.0.6          tools_4.5.0               
+##  [53] progress_1.2.3             ragg_1.3.0                
+##  [55] Rcpp_1.0.12                glue_1.7.0                
+##  [57] gridExtra_2.3              SparseArray_1.3.4         
+##  [59] xfun_0.43                  withr_3.0.0               
+##  [61] formatR_1.14               BiocManager_1.30.22       
+##  [63] fastmap_1.1.1              latticeExtra_0.6-30       
+##  [65] fansi_1.0.6                digest_0.6.35             
+##  [67] timechange_0.3.0           R6_2.5.1                  
+##  [69] textshaping_0.3.7          colorspace_2.1-0          
+##  [71] jpeg_0.1-10                dichromat_2.0-0.1         
+##  [73] biomaRt_2.59.1             RSQLite_2.3.6             
+##  [75] utf8_1.2.4                 generics_0.1.3            
+##  [77] data.table_1.15.4          rtracklayer_1.63.2        
+##  [79] prettyunits_1.2.0          InteractionSet_1.31.0     
+##  [81] httr_1.4.7                 htmlwidgets_1.6.4         
+##  [83] S4Arrays_1.3.6             pkgconfig_2.0.3           
+##  [85] gtable_0.3.4               blob_1.2.4                
+##  [87] XVector_0.43.1             htmltools_0.5.8.1         
+##  [89] bookdown_0.38              ProtGenerics_1.35.4       
+##  [91] scales_1.3.0               png_0.1-8                 
+##  [93] knitr_1.46                 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_1.0.8              
+## [101] parallel_4.5.0             foreign_0.8-86            
+## [103] AnnotationDbi_1.65.2       restfulr_0.0.15           
+## [105] desc_1.4.3                 pillar_1.9.0              
+## [107] grid_4.5.0                 vctrs_0.6.5               
+## [109] dbplyr_2.5.0               cluster_2.1.6             
+## [111] htmlTable_2.4.2            evaluate_0.23             
+## [113] VennDiagram_1.7.3          GenomicFeatures_1.55.4    
+## [115] cli_3.6.2                  locfit_1.5-9.9            
+## [117] compiler_4.5.0             futile.options_1.0.1      
+## [119] Rsamtools_2.19.4           rlang_1.1.3               
+## [121] crayon_1.5.2               interp_1.1-6              
+## [123] fs_1.6.3                   stringi_1.8.3             
+## [125] deldir_2.0-4               munsell_0.5.1             
+## [127] Biostrings_2.71.5          lazyeval_0.2.2            
+## [129] csaw_1.37.1                Matrix_1.7-0              
+## [131] BSgenome_1.71.4            hms_1.1.3                 
+## [133] patchwork_1.2.0            bit64_4.0.5               
+## [135] KEGGREST_1.43.0            statmod_1.5.0             
+## [137] highr_0.10                 igraph_2.0.3              
+## [139] broom_1.0.5                memoise_2.0.1             
+## [141] bslib_0.7.0                bit_4.0.5                 
+## [143] GenomicInteractions_1.37.0
diff --git a/authors.html b/authors.html index 668d2fa..d1b54e1 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 @@ -79,13 +79,13 @@

Citation

Pederson S (2024). extraChIPs: Additional functions for working with ChIP-Seq data. -R package version 1.7.6, https://github.com/smped/extraChIPs. +R package version 1.7.7, 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 1.7.6},
+  note = {R package version 1.7.7},
   url = {https://github.com/smped/extraChIPs},
 }
diff --git a/index.html b/index.html index 9f373ab..2d8c143 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/news/index.html b/news/index.html index 0310db4..305d38d 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 @@ -187,7 +187,13 @@

Cha

Changes in 1.7.6

-
  • Added the DESeq2 Wald statistic to options for fitAssayDiff
    • +
+
+

Changes in 1.7.7

+
  • Added merge_within to makeConsensus() for better handling when method = "coverage" +
diff --git a/pkgdown.yml b/pkgdown.yml index 1724ab1..68a4915 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,5 +5,5 @@ articles: differential_signal_fixed: differential_signal_fixed.html differential_signal_sliding: differential_signal_sliding.html range_based_functions: range_based_functions.html -last_built: 2024-04-02T16:30Z +last_built: 2024-04-07T03:07Z diff --git a/reference/addDiffStatus-methods.html b/reference/addDiffStatus-methods.html index 9b6b133..fdbe8b6 100644 --- a/reference/addDiffStatus-methods.html +++ b/reference/addDiffStatus-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/as_tibble.html b/reference/as_tibble.html index 38fac4b..c3309dd 100644 --- a/reference/as_tibble.html +++ b/reference/as_tibble.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/bestOverlap-methods.html b/reference/bestOverlap-methods.html index 7404793..ec15f54 100644 --- a/reference/bestOverlap-methods.html +++ b/reference/bestOverlap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/chopMC.html b/reference/chopMC.html index 36dbd1b..2964fc5 100644 --- a/reference/chopMC.html +++ b/reference/chopMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/colToRanges-methods.html b/reference/colToRanges-methods.html index d6d3541..7c7a84a 100644 --- a/reference/colToRanges-methods.html +++ b/reference/colToRanges-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/collapseGenes.html b/reference/collapseGenes.html index 75fbce3..b7b07f2 100644 --- a/reference/collapseGenes.html +++ b/reference/collapseGenes.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/cytobands.html b/reference/cytobands.html index ad8b544..1edf33b 100644 --- a/reference/cytobands.html +++ b/reference/cytobands.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/defineRegions.html b/reference/defineRegions.html index b19dc4f..269ae15 100644 --- a/reference/defineRegions.html +++ b/reference/defineRegions.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/defineSeqinfo.html b/reference/defineSeqinfo.html index 9c05c94..adcf8f6 100644 --- a/reference/defineSeqinfo.html +++ b/reference/defineSeqinfo.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/distinctMC.html b/reference/distinctMC.html index c644224..71545f0 100644 --- a/reference/distinctMC.html +++ b/reference/distinctMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/dot-makeFinalProfileHeatmap.html b/reference/dot-makeFinalProfileHeatmap.html index 65117b2..1d2925c 100644 --- a/reference/dot-makeFinalProfileHeatmap.html +++ b/reference/dot-makeFinalProfileHeatmap.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/dot-mapFeatures.html b/reference/dot-mapFeatures.html index 0cd8ddd..6601606 100644 --- a/reference/dot-mapFeatures.html +++ b/reference/dot-mapFeatures.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/dot-mapGi.html b/reference/dot-mapGi.html index c35b28f..012c4c9 100644 --- a/reference/dot-mapGi.html +++ b/reference/dot-mapGi.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/dot-mapWithin.html b/reference/dot-mapWithin.html index 521464f..28b06b4 100644 --- a/reference/dot-mapWithin.html +++ b/reference/dot-mapWithin.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/dualFilter.html b/reference/dualFilter.html index acd83f0..6824f92 100644 --- a/reference/dualFilter.html +++ b/reference/dualFilter.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/ex_datasets.html b/reference/ex_datasets.html index 8cb5488..0dcf054 100644 --- a/reference/ex_datasets.html +++ b/reference/ex_datasets.html @@ -37,7 +37,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/extraChIPs-package.html b/reference/extraChIPs-package.html index 4384dac..0c86db8 100644 --- a/reference/extraChIPs-package.html +++ b/reference/extraChIPs-package.html @@ -19,7 +19,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/fitAssayDiff-methods.html b/reference/fitAssayDiff-methods.html index 7db9f1e..447593b 100644 --- a/reference/fitAssayDiff-methods.html +++ b/reference/fitAssayDiff-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/fixed_width_datasets.html b/reference/fixed_width_datasets.html index e7eafce..3f51ec0 100644 --- a/reference/fixed_width_datasets.html +++ b/reference/fixed_width_datasets.html @@ -19,7 +19,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/getProfileData-methods.html b/reference/getProfileData-methods.html index 2563213..210b3b4 100644 --- a/reference/getProfileData-methods.html +++ b/reference/getProfileData-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/grlToSE-methods.html b/reference/grlToSE-methods.html index 2b58c01..c92490b 100644 --- a/reference/grlToSE-methods.html +++ b/reference/grlToSE-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/importPeaks.html b/reference/importPeaks.html index 99094a0..432e3da 100644 --- a/reference/importPeaks.html +++ b/reference/importPeaks.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/index.html b/reference/index.html index 418ae02..e4a6e2a 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/makeConsensus.html b/reference/makeConsensus.html index 62d3999..23a0fbb 100644 --- a/reference/makeConsensus.html +++ b/reference/makeConsensus.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 @@ -77,6 +77,7 @@

Make a set of consensus peaks

ignore.strand = TRUE, simplify = FALSE, min_width = 0, + merge_within = 1L, ... ) @@ -112,6 +113,10 @@

Arguments

min_width

Discard any regions below this width

+ +
merge_within
+

Passed to reduce as min.gapwidth

+

Value

@@ -135,10 +140,10 @@

Details

range which are 'covered' by the minimum proportion of replicates specified are returned. This will return narrower peaks in general, although some artefactual very small ranges may be included (e.g. 10bp). Careful setting -of the min_width parameter may be very helpful for these instances. It is -also expected that setting method = "coverage" should return the region -within each range which is more likely to contain the true binding site for -the relevant ChIP targets

+of the min_width and merge_within parameters may be very helpful for these +instances. It is also expected that setting method = "coverage" should return +the region within each range which is more likely to contain the true binding +site for the relevant ChIP targets

See also

diff --git a/reference/mapByFeature.html b/reference/mapByFeature.html index f9869be..1dbe53c 100644 --- a/reference/mapByFeature.html +++ b/reference/mapByFeature.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7
diff --git a/reference/mapGrlCols.html b/reference/mapGrlCols.html index 24672a2..81e4fe5 100644 --- a/reference/mapGrlCols.html +++ b/reference/mapGrlCols.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/mergeByCol-methods.html b/reference/mergeByCol-methods.html index ea7f580..98c6a05 100644 --- a/reference/mergeByCol-methods.html +++ b/reference/mergeByCol-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/mergeByHMP-methods.html b/reference/mergeByHMP-methods.html index eabc13c..f2e4da3 100644 --- a/reference/mergeByHMP-methods.html +++ b/reference/mergeByHMP-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/mergeBySig-methods.html b/reference/mergeBySig-methods.html index 0714c1d..815ba5d 100644 --- a/reference/mergeBySig-methods.html +++ b/reference/mergeBySig-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/partitionRanges-methods.html b/reference/partitionRanges-methods.html index d01f38f..16de7a3 100644 --- a/reference/partitionRanges-methods.html +++ b/reference/partitionRanges-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotAssayDensities-methods.html b/reference/plotAssayDensities-methods.html index eb12989..fc29746 100644 --- a/reference/plotAssayDensities-methods.html +++ b/reference/plotAssayDensities-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotAssayHeatmap-methods.html b/reference/plotAssayHeatmap-methods.html index dbab69b..81b2aee 100644 --- a/reference/plotAssayHeatmap-methods.html +++ b/reference/plotAssayHeatmap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotAssayPCA-methods.html b/reference/plotAssayPCA-methods.html index 49482ed..a886b9d 100644 --- a/reference/plotAssayPCA-methods.html +++ b/reference/plotAssayPCA-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotAssayRle-methods.html b/reference/plotAssayRle-methods.html index 74bcae7..376ec7c 100644 --- a/reference/plotAssayRle-methods.html +++ b/reference/plotAssayRle-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotGrlCol.html b/reference/plotGrlCol.html index cfc0c77..355c8cb 100644 --- a/reference/plotGrlCol.html +++ b/reference/plotGrlCol.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotHFGC.html b/reference/plotHFGC.html index e74f69f..548d22b 100644 --- a/reference/plotHFGC.html +++ b/reference/plotHFGC.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotOverlaps-methods.html b/reference/plotOverlaps-methods.html index 204ac53..33c0bf2 100644 --- a/reference/plotOverlaps-methods.html +++ b/reference/plotOverlaps-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 @@ -83,7 +83,7 @@

Plot Overlaps Between List Elements

hj_sets = 1.15, sz_sets = 3.5, exp_sets = 0.25, - min.gapwidth = 1L, + merge_within = 1L, ignore.strand = TRUE ) @@ -147,7 +147,11 @@

Arguments

X-axis expansion for set size panel

-
min.gapwidth, ignore.strand
+
merge_within
+

Passed to makeConsensus

+ + +
ignore.strand

Passed to reduce

diff --git a/reference/plotPairwise.html b/reference/plotPairwise.html index cb3b212..73a1906 100644 --- a/reference/plotPairwise.html +++ b/reference/plotPairwise.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotPie-methods.html b/reference/plotPie-methods.html index d18083f..8561325 100644 --- a/reference/plotPie-methods.html +++ b/reference/plotPie-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotProfileHeatmap-methods.html b/reference/plotProfileHeatmap-methods.html index bb798c8..c7e94b2 100644 --- a/reference/plotProfileHeatmap-methods.html +++ b/reference/plotProfileHeatmap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/plotSplitDonut-methods.html b/reference/plotSplitDonut-methods.html index 9e3fb7e..1623167 100644 --- a/reference/plotSplitDonut-methods.html +++ b/reference/plotSplitDonut-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/propOverlap-methods.html b/reference/propOverlap-methods.html index 9533d92..2162f3e 100644 --- a/reference/propOverlap-methods.html +++ b/reference/propOverlap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/reduceMC.html b/reference/reduceMC.html index 922b53d..ead2b0a 100644 --- a/reference/reduceMC.html +++ b/reference/reduceMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/setoptsMC-methods.html b/reference/setoptsMC-methods.html index 8f65a06..50dfeae 100644 --- a/reference/setoptsMC-methods.html +++ b/reference/setoptsMC-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/stitchRanges.html b/reference/stitchRanges.html index 07cc48d..b6b8acb 100644 --- a/reference/stitchRanges.html +++ b/reference/stitchRanges.html @@ -18,7 +18,7 @@ extraChIPs - 1.7.6 + 1.7.7 diff --git a/reference/voomWeightsFromCPM.html b/reference/voomWeightsFromCPM.html index e5be358..b3628d9 100644 --- a/reference/voomWeightsFromCPM.html +++ b/reference/voomWeightsFromCPM.html @@ -17,7 +17,7 @@ extraChIPs - 1.7.6 + 1.7.7