geneAccessibility: Find the accessibility of the peaks overlapping a set of...

In FertigLab/ATACCoGAPS: Analysis Tools for scATACseq Data with CoGAPS

Find the accessibility of the peaks overlapping a set of genes and their promoters

Description

The accessibility of a particular set of interest genes is checked by testing overlap of peaks with the genes and gene promoters and then returning the binarized accesibility data for those peaks

Usage

geneAccessibility(geneList, peakGranges, atacData, genome)

Arguments

geneList	vector of HGNC gene symbols to find overlapping peaks for in the data
peakGranges	a GRanges object corresponding to the peaks in the atacData matrix, in the same order as the rows of the atacData matrix
atacData	a single-cell ATAC-seq count matrix peaks by cells
genome	TxDb object to produce gene GRanges from

Value

List of matrices corresponding to the accessible peaks overlapping with each gene across all cells in the data

Examples

library(Homo.sapiens)
geneList <- c("TAL1", "IRF1")
data(schepGranges)
data("subsetSchepData")
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges,
 atacData = subsetSchepData, genome = Homo.sapiens)

FertigLab/ATACCoGAPS documentation built on Feb. 8, 2023, 6:46 p.m.