genomicRegions: Genomic Regions

Description Usage Arguments See Also Examples

Description

From a list of genes chromosomes tss and strandedness split the genome into mutualy exclusive regions defined by the gene regions of influence These regions can be used to relate ChIP binding data to genes. This function combines the geneRagnges and geneRangeToRegion function into a single form.

Usage

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genomicRegions(chrom, tss, strand, proxUp, proxDown, distal,
  n = length(chrom), chroms = unique(chrom))

Arguments

chrom

A list of chromosomes, one for each gene

tss

The list of gene TSS

strand

The stream directions of each of the genes

proxUp

Upstream basal extension (independent of other genes)

proxDown

Downstream basal extension (independent of other genes)

distal

The limit of gene extension (in either direction)

See Also

geneRanges

Examples

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heightFile<-"peaks/jan/combined_heights.bed"
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)

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