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Export bigwig files from split fragments file with tests #1887

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Merged
timoast merged 8 commits into from
Jun 11, 2026
Merged

Export bigwig files from split fragments file with tests #1887

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c8503b5
Add ExportGroupBW to export per-group bigwig files (#1887)
Jun 11, 2026
78b81b5
Rename ExportGroupBW to ExportBigwig and address review
timoast Jun 11, 2026
ba2de7a
Validate ExportBigwig normalization column and empty group set
timoast Jun 11, 2026
1c15445
Use true per-group cell count for ncells normalization
timoast Jun 11, 2026
9cfc33a
Use markdown formatting in ExportBigwig documentation
timoast Jun 11, 2026
3988ef1
Default ExportBigwig outdir to the current working directory
timoast Jun 11, 2026
d0f1fec
Write ExportBigwig intermediate bed files to a temporary directory
timoast Jun 11, 2026
462c509
Add ExportBigwig to NEWS and pkgdown, fix example
timoast Jun 11, 2026
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3 changes: 2 additions & 1 deletion DESCRIPTION
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Expand Up @@ -65,10 +65,11 @@ Imports:
Collate:
'RcppExports.R'
'Signac-package.R'
'generics.R'
'bigwig.R'
'classes.R'
'data.R'
'differential_accessibility.R'
'generics.R'
'dimension_reduction.R'
'footprinting.R'
'fragments.R'
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2 changes: 2 additions & 0 deletions NAMESPACE
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Expand Up @@ -172,6 +172,7 @@ export(DensityScatter)
export(DepthCor)
export(DownsampleFeatures)
export(EnrichedTerms)
export(ExportBigwig)
export(ExpressionPlot)
export(Extend)
export(FRiP)
Expand Down Expand Up @@ -296,6 +297,7 @@ importFrom(GenomicRanges,makeGRangesFromDataFrame)
importFrom(GenomicRanges,reduce)
importFrom(GenomicRanges,resize)
importFrom(GenomicRanges,seqnames)
importFrom(GenomicRanges,slidingWindows)
importFrom(GenomicRanges,start)
importFrom(GenomicRanges,strand)
importFrom(GenomicRanges,tileGenome)
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1 change: 1 addition & 0 deletions NEWS.md
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Expand Up @@ -60,6 +60,7 @@ regions side-by-side with shared formatting and axis labels
* Added `ReadMQuad()` function to import output from [MQuad](https://github.com/single-cell-genetics/MQuad) for mitochondrial variant analysis
* Added `ReadPWM()` function to read `.pwm` files from a directory into a `PWMatrixList`
* Added `ReadJASPAR()` function to read motifs from a JASPAR-format file into a `PWMatrixList`
* Added `ExportBigwig()` function to export per-group Tn5 insertion coverage tracks as bigwig files

Removed functions:

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