foldAccessibility: Estimate fold Accessibility of a Gene Relative to Average

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

Estimate fold Accessibility of a Gene Relative to Average

Description

Compares the accessibility of peaks overlapping with a gene, as returned by the geneAccessibility function to the average accessibility of peaks within a given cell population. Meant to provide a rough estimate of how accessible a gene is with values higher than 1 providing evidence of differential accessibility (and thus implying possible transcription), with values lower than 1 indicating the opposite.

Usage

foldAccessibility(peaksAccessibility, cellTypeList, cellType, binaryMatrix)

Arguments

peaksAccessibility	the binarized accessibility of a set of peaks; one value returned from the geneAccessibility function
cellTypeList	list of celltypes grouping cells in the data
cellType	the particular cell type of interest from within cellTypeList
binaryMatrix	binarized scATAC data matrix

Value

Fold accessibility value as compared to average peaks for a given cell type

Examples

data("subsetSchepData")
data(schepCellTypes)
library(Homo.sapiens)
geneList <- c("TAL1", "IRF1")
data(schepGranges)
binarizedData <- (subsetSchepData > 0) + 0
accessiblePeaks <- geneAccessibility(geneList = geneList, peakGranges = schepGranges,
 atacData = subsetSchepData, genome = Homo.sapiens)
foldAccessibility(peaksAccessibility = accessiblePeaks$TAL1, cellTypeList = schepCellTypes,
 cellType = "K562 Erythroleukemia", binaryMatrix = binarizedData)

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