RegionChromVAR: Run chromVAR on a subset of peaks overlapping a list of...
In yanwu2014/chromfunks: Functions for Analyzing Chromatin Accessibility Data
View source: R/region_enrich.R
RegionChromVAR R Documentation
Run chromVAR on a subset of peaks overlapping a list of regions
Description
Run chromVAR on a subset of peaks overlapping a list of regions
Usage
RegionChromVAR(SE, motif_ix, regionList, n.runs)
Arguments
SE
Peaks accessibility matrix in SummarizedExperiment format
motif_ix
Transcription factor motif data in SummarizedExperiment format (from motifmatchr)
n.runs
Number of replicates to run
regionsList
List of regions in GenomicRanges format
Value
For each set of regions z-scores representing the enrichment of TF motifs in peaks overlapping those regions for each column in SE
yanwu2014/chromfunks documentation built on Aug. 20, 2023, 9:17 a.m.
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View source: R/region_enrich.R
| RegionChromVAR | R Documentation |
Run chromVAR on a subset of peaks overlapping a list of regions
Description
Run chromVAR on a subset of peaks overlapping a list of regions
Usage
RegionChromVAR(SE, motif_ix, regionList, n.runs)
Arguments
SE |
Peaks accessibility matrix in SummarizedExperiment format |
motif_ix |
Transcription factor motif data in SummarizedExperiment format (from motifmatchr) |
n.runs |
Number of replicates to run |
regionsList |
List of regions in GenomicRanges format |
Value
For each set of regions z-scores representing the enrichment of TF motifs in peaks overlapping those regions for each column in SE
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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