greatGeneAssoc: Great Gene Assoc

In alexjgriffith/CCCA: Cross Condition ChIP Analyisis

Description

Compare peak locations to predetermined genomic regions and return a list of genes that corospond to the overlaped gene regions. This function acts as a filter for a gene list whose indicies are shared with the gene regions. Only the genes within regions that have peaks are returned.

Usage

greatGeneAssoc(bedData, genes, geneList)

Arguments

bedData	The binding locations of interest
genes	The genome split into gene regions
geneList	A list with a 1-1 relation to the gene regions

Value

A filtered geneList

Examples

bedFile<-"peaks/jan/combined.bed"
bed<-read.delim(bedFile)
geneFile<-"~/hg19.RefSeqGenes.csv"
geneList<-read.delim(geneFile)
chrom<-as.character(geneList$chrom)
tss<-as.numeric(geneList$txStart)
strand<-geneList$strand
# double check to make sure that levels(strand) > c("-","+")
levels(strand)<-c(-1,1)
strand<-as.numeric(strand)
statsAndData<-readSplitTable(heightFile)
regions<-genomicRegions(chrom,tss,strand,1000,5000,1000000)
genes<-greatGeneAssoc(bed,regions,geneList)

alexjgriffith/CCCA documentation built on May 10, 2019, 8:52 a.m.