Description Usage Arguments Value Examples
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.
1 | greatGeneAssoc(bedData, genes, geneList)
|
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 |
A filtered geneList
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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)
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