genePatternMatch: Match genes to pattern differentiating peaks

View source: R/genePeakMatchingv2.R

genePatternMatchR Documentation

Match genes to pattern differentiating peaks

Description

Function to take as input CoGAPS results for ATAC-seq data and find genes within the most "pattern-defining" regions (as identified by cut thresholded pattern Marker statistic from the CoGAPS package), as well as the nearest gene and the nearest gene following the region. Note: a TxDb object for the genome of interest must be loaded prior to running this function.

Usage

genePatternMatch(cogapsResult, generanges, genome, scoreThreshold = NULL)

Arguments

cogapsResult

the CogapsResult object produced by a CoGAPS run

generanges

GRanges object corresponding to the genomic regions identified as peaks for the ATAC-seq data that CoGAPS was run on

genome

A TxDb object for the genome of interest, it must be loaded prior to calling this function

scoreThreshold

threshold for the most pattern defining peaks as per the PatternMarker statistic from the CoGAPS package. Default is NULL, returning all PatternMarker peaks. Useful to reduce computational time, as top results are reasonably robust to using more stringent thresholds

Value

double nested list containing lists of the genes in, nearest, and following the peaks matched each pattern

Examples

data("schepCogapsResult")
data(schepGranges)

library(Homo.sapiens)

genes = genePatternMatch(cogapsResult = schepCogapsResult,
 generanges = schepGranges, genome = Homo.sapiens)

FertigLab/ATACCoGAPS documentation built on June 29, 2022, 4:13 p.m.