mapPeaksToGenes: Map peaks to genes

In PFPrzytycki/CellWalkR: An R Package for Integrating and Visualizing Single-Cell and Bulk Data to Resolve Regulatory Elements

Map peaks to genes

Description

mapPeaksToGenes Generates a mapping from genes to peaks per label

Usage

mapPeaksToGenes(labelGenes, ATACMat, peaks, regions)

Arguments

labelGenes	data.frame with genes of interest in first column and corresponding labels in second column
ATACMat	cell-by-peak matrix
peaks	GRanges object of peaks (equal to number of rows in ATACMat)
regions	GRanges object of genomic regions associated with genes

Value

list of genes and corresponding peaks by label

Examples

data("SampleCellWalkRData")
regions <- getRegions()
mapPeaksToGenes(SampleCellWalkRData$labelGenes,
                SampleCellWalkRData$ATACMat,
                SampleCellWalkRData$peaks,
                regions)

PFPrzytycki/CellWalkR documentation built on Oct. 26, 2023, 1:50 p.m.