From 420c512d722478407ccef4cf4c9fc7c39aa85809 Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sat, 27 Jul 2024 12:10:36 +0000 Subject: [PATCH] Built site for extraChIPs@1.9.4: 7cb5a8e --- 404.html | 2 +- articles/differential_signal_fixed.html | 6 +++--- articles/differential_signal_sliding.html | 6 +++--- articles/index.html | 2 +- articles/range_based_functions.html | 6 +++--- authors.html | 6 +++--- index.html | 2 +- news/index.html | 2 +- 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 | 9 +++++++-- 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 | 2 +- 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 | 2 +- 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, 69 insertions(+), 64 deletions(-) diff --git a/404.html b/404.html index 95f53a6..8f44494 100644 --- a/404.html +++ b/404.html @@ -32,7 +32,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/articles/differential_signal_fixed.html b/articles/differential_signal_fixed.html index 425c96e..3a7ccfb 100644 --- a/articles/differential_signal_fixed.html +++ b/articles/differential_signal_fixed.html @@ -32,7 +32,7 @@ extraChIPs - 1.8.3 + 1.9.4 @@ -761,7 +761,7 @@

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_1.8.3 ggside_0.3.1 +## [7] extraChIPs_1.9.4 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 @@ -857,7 +857,7 @@

Session Info## [151] lambda.r_1.2.4 BiocManager_1.30.23 ## [153] tzdb_0.4.0 foreach_1.5.2 ## [155] tweenr_2.0.3 openssl_2.2.0 -## [157] polyclip_1.10-6 reshape_0.8.9 +## [157] polyclip_1.10-7 reshape_0.8.9 ## [159] ggforce_0.4.2 broom_1.0.6 ## [161] xtable_1.8-4 restfulr_0.0.15 ## [163] AnnotationFilter_1.28.0 ragg_1.3.2 diff --git a/articles/differential_signal_sliding.html b/articles/differential_signal_sliding.html index ce01391..c2c158b 100644 --- a/articles/differential_signal_sliding.html +++ b/articles/differential_signal_sliding.html @@ -32,7 +32,7 @@ extraChIPs - 1.8.3 + 1.9.4 @@ -1301,7 +1301,7 @@

Session Info## [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 +## [7] plyranges_1.24.0 extraChIPs_1.9.4 ## [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 @@ -1395,7 +1395,7 @@

Session Info## [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 +## [153] openssl_2.2.0 polyclip_1.10-7 ## [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 diff --git a/articles/index.html b/articles/index.html index 83ee8e8..f9f6d83 100644 --- a/articles/index.html +++ b/articles/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/articles/range_based_functions.html b/articles/range_based_functions.html index 07a4de1..a786be6 100644 --- a/articles/range_based_functions.html +++ b/articles/range_based_functions.html @@ -32,7 +32,7 @@ extraChIPs - 1.8.3 + 1.9.4 @@ -666,7 +666,7 @@

Session Info## [8] base ## ## other attached packages: -## [1] plyranges_1.24.0 extraChIPs_1.8.3 +## [1] plyranges_1.24.0 extraChIPs_1.9.4 ## [3] SummarizedExperiment_1.34.0 Biobase_2.64.0 ## [5] MatrixGenerics_1.16.0 matrixStats_1.3.0 ## [7] ggside_0.3.1 GenomicRanges_1.56.1 @@ -681,7 +681,7 @@

Session Info## ## 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 +## [3] filelock_1.0.3 polyclip_1.10-7 ## [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 diff --git a/authors.html b/authors.html index 0928f03..145e6e8 100644 --- a/authors.html +++ b/authors.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 @@ -79,13 +79,13 @@

Citation

Pederson S (2024). extraChIPs: Additional functions for working with ChIP-Seq data. -R package version 1.8.3, https://github.com/smped/extraChIPs. +R package version 1.9.4, 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 1.8.3},
+  note = {R package version 1.9.4},
   url = {https://github.com/smped/extraChIPs},
 }
diff --git a/index.html b/index.html index 3bd4a80..7fa4a32 100644 --- a/index.html +++ b/index.html @@ -33,7 +33,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/news/index.html b/news/index.html index 5872530..e081a63 100644 --- a/news/index.html +++ b/news/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/pkgdown.yml b/pkgdown.yml index 5540bde..7dca0d1 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -5,4 +5,4 @@ articles: differential_signal_fixed: differential_signal_fixed.html differential_signal_sliding: differential_signal_sliding.html range_based_functions: range_based_functions.html -last_built: 2024-07-23T14:27Z +last_built: 2024-07-27T12:08Z diff --git a/reference/addDiffStatus-methods.html b/reference/addDiffStatus-methods.html index fee4799..4b45467 100644 --- a/reference/addDiffStatus-methods.html +++ b/reference/addDiffStatus-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/as_tibble.html b/reference/as_tibble.html index 4185609..cb3c42b 100644 --- a/reference/as_tibble.html +++ b/reference/as_tibble.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/bestOverlap-methods.html b/reference/bestOverlap-methods.html index 014902b..c2809f5 100644 --- a/reference/bestOverlap-methods.html +++ b/reference/bestOverlap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/chopMC.html b/reference/chopMC.html index 9e43a9d..ec9f3aa 100644 --- a/reference/chopMC.html +++ b/reference/chopMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/colToRanges-methods.html b/reference/colToRanges-methods.html index a78e8e5..8db6bc6 100644 --- a/reference/colToRanges-methods.html +++ b/reference/colToRanges-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 @@ -75,7 +75,7 @@

Coerce a column to a GRanges object

colToRanges(x, var, seqinfo = NULL, ...) # S4 method for class 'GRanges' -colToRanges(x, var, ...) +colToRanges(x, var, ..., keep_metadata = TRUE) # S4 method for class 'data.frame' colToRanges(x, var, seqinfo = NULL, ...) @@ -101,6 +101,11 @@

Arguments

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

+ +
keep_metadata
+

logical(1) If the original object is a GRanges object, +retain all metadata from the original ranges in the replaced ranges

+

Value

diff --git a/reference/collapseGenes.html b/reference/collapseGenes.html index fa11ed2..b0b0874 100644 --- a/reference/collapseGenes.html +++ b/reference/collapseGenes.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4
diff --git a/reference/cytobands.html b/reference/cytobands.html index 5ac22ae..7e75861 100644 --- a/reference/cytobands.html +++ b/reference/cytobands.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/defineRegions.html b/reference/defineRegions.html index e2f801d..d2e4156 100644 --- a/reference/defineRegions.html +++ b/reference/defineRegions.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/defineSeqinfo.html b/reference/defineSeqinfo.html index b0b7a31..d0e3891 100644 --- a/reference/defineSeqinfo.html +++ b/reference/defineSeqinfo.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/distinctMC.html b/reference/distinctMC.html index 573c785..a36d2bb 100644 --- a/reference/distinctMC.html +++ b/reference/distinctMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/dot-makeFinalProfileHeatmap.html b/reference/dot-makeFinalProfileHeatmap.html index 4bb2d84..9e0c70b 100644 --- a/reference/dot-makeFinalProfileHeatmap.html +++ b/reference/dot-makeFinalProfileHeatmap.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/dot-mapFeatures.html b/reference/dot-mapFeatures.html index dbc647a..c287833 100644 --- a/reference/dot-mapFeatures.html +++ b/reference/dot-mapFeatures.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/dot-mapGi.html b/reference/dot-mapGi.html index de82f6f..babaee5 100644 --- a/reference/dot-mapGi.html +++ b/reference/dot-mapGi.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/dot-mapWithin.html b/reference/dot-mapWithin.html index 94c6fb5..5046853 100644 --- a/reference/dot-mapWithin.html +++ b/reference/dot-mapWithin.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/dualFilter.html b/reference/dualFilter.html index d1f535c..607ae77 100644 --- a/reference/dualFilter.html +++ b/reference/dualFilter.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/ex_datasets.html b/reference/ex_datasets.html index 28fd5c6..702eb4b 100644 --- a/reference/ex_datasets.html +++ b/reference/ex_datasets.html @@ -37,7 +37,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/extraChIPs-package.html b/reference/extraChIPs-package.html index 0414155..0ceba70 100644 --- a/reference/extraChIPs-package.html +++ b/reference/extraChIPs-package.html @@ -19,7 +19,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/fitAssayDiff-methods.html b/reference/fitAssayDiff-methods.html index 1022548..c4c04cb 100644 --- a/reference/fitAssayDiff-methods.html +++ b/reference/fitAssayDiff-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/fixed_width_datasets.html b/reference/fixed_width_datasets.html index 95b9aef..e1e3850 100644 --- a/reference/fixed_width_datasets.html +++ b/reference/fixed_width_datasets.html @@ -19,7 +19,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/getProfileData-methods.html b/reference/getProfileData-methods.html index 7de201b..6494ca9 100644 --- a/reference/getProfileData-methods.html +++ b/reference/getProfileData-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/grlToSE-methods.html b/reference/grlToSE-methods.html index 5bb646b..d61adb9 100644 --- a/reference/grlToSE-methods.html +++ b/reference/grlToSE-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/importPeaks.html b/reference/importPeaks.html index fa63898..c18c75d 100644 --- a/reference/importPeaks.html +++ b/reference/importPeaks.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/index.html b/reference/index.html index 5907c5e..b2aca6f 100644 --- a/reference/index.html +++ b/reference/index.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/makeConsensus.html b/reference/makeConsensus.html index 88cf25a..c90df58 100644 --- a/reference/makeConsensus.html +++ b/reference/makeConsensus.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/mapByFeature.html b/reference/mapByFeature.html index dbf6326..1c50323 100644 --- a/reference/mapByFeature.html +++ b/reference/mapByFeature.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/mapGrlCols.html b/reference/mapGrlCols.html index 4179888..9fbd9fa 100644 --- a/reference/mapGrlCols.html +++ b/reference/mapGrlCols.html @@ -18,7 +18,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/mergeByCol-methods.html b/reference/mergeByCol-methods.html index d7da362..1e64422 100644 --- a/reference/mergeByCol-methods.html +++ b/reference/mergeByCol-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/mergeByHMP-methods.html b/reference/mergeByHMP-methods.html index 13225d3..95dde3a 100644 --- a/reference/mergeByHMP-methods.html +++ b/reference/mergeByHMP-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/mergeBySig-methods.html b/reference/mergeBySig-methods.html index d652013..3c58d22 100644 --- a/reference/mergeBySig-methods.html +++ b/reference/mergeBySig-methods.html @@ -18,7 +18,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/partitionRanges-methods.html b/reference/partitionRanges-methods.html index 66a4885..667bd40 100644 --- a/reference/partitionRanges-methods.html +++ b/reference/partitionRanges-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotAssayDensities-methods.html b/reference/plotAssayDensities-methods.html index 5a26093..360b5c8 100644 --- a/reference/plotAssayDensities-methods.html +++ b/reference/plotAssayDensities-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotAssayHeatmap-methods.html b/reference/plotAssayHeatmap-methods.html index 008637a..f29a9cd 100644 --- a/reference/plotAssayHeatmap-methods.html +++ b/reference/plotAssayHeatmap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotAssayPCA-methods.html b/reference/plotAssayPCA-methods.html index b100c19..d631df4 100644 --- a/reference/plotAssayPCA-methods.html +++ b/reference/plotAssayPCA-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotAssayRle-methods.html b/reference/plotAssayRle-methods.html index 6cb5b47..17fc626 100644 --- a/reference/plotAssayRle-methods.html +++ b/reference/plotAssayRle-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotGrlCol.html b/reference/plotGrlCol.html index 371fbea..6971093 100644 --- a/reference/plotGrlCol.html +++ b/reference/plotGrlCol.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotHFGC.html b/reference/plotHFGC.html index 8c41308..1df9195 100644 --- a/reference/plotHFGC.html +++ b/reference/plotHFGC.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotOverlaps-methods.html b/reference/plotOverlaps-methods.html index 8154bd2..e6dada3 100644 --- a/reference/plotOverlaps-methods.html +++ b/reference/plotOverlaps-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotPairwise.html b/reference/plotPairwise.html index ac78aa4..f804be9 100644 --- a/reference/plotPairwise.html +++ b/reference/plotPairwise.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotPie-methods.html b/reference/plotPie-methods.html index b350f23..a22c1a4 100644 --- a/reference/plotPie-methods.html +++ b/reference/plotPie-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotProfileHeatmap-methods.html b/reference/plotProfileHeatmap-methods.html index 07ad1c9..b919a02 100644 --- a/reference/plotProfileHeatmap-methods.html +++ b/reference/plotProfileHeatmap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/plotSplitDonut-methods.html b/reference/plotSplitDonut-methods.html index 73bb515..8287a3b 100644 --- a/reference/plotSplitDonut-methods.html +++ b/reference/plotSplitDonut-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/propOverlap-methods.html b/reference/propOverlap-methods.html index 1b5011c..25abd43 100644 --- a/reference/propOverlap-methods.html +++ b/reference/propOverlap-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/reduceMC.html b/reference/reduceMC.html index 374cf75..01ddc33 100644 --- a/reference/reduceMC.html +++ b/reference/reduceMC.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/setoptsMC-methods.html b/reference/setoptsMC-methods.html index 966aeb2..8e88dbd 100644 --- a/reference/setoptsMC-methods.html +++ b/reference/setoptsMC-methods.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/stitchRanges.html b/reference/stitchRanges.html index a6402a5..c0d2192 100644 --- a/reference/stitchRanges.html +++ b/reference/stitchRanges.html @@ -18,7 +18,7 @@ extraChIPs - 1.8.3 + 1.9.4 diff --git a/reference/voomWeightsFromCPM.html b/reference/voomWeightsFromCPM.html index e851437..fd2738e 100644 --- a/reference/voomWeightsFromCPM.html +++ b/reference/voomWeightsFromCPM.html @@ -17,7 +17,7 @@ extraChIPs - 1.8.3 + 1.9.4