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
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
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_1.37.0Pederson 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 @@
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 @@
@@ -187,7 +187,13 @@ fitAssayDiff()
+merge_within to makeConsensus() for better handling when method = "coverage"
+Discard any regions below this width
Passed to reduce as min.gapwidth
X-axis expansion for set size panel
Passed to makeConsensus
Passed to reduce