genomicRegions: Genomic Regions
In alexjgriffith/CCCA: Cross Condition ChIP Analyisis

Description Usage Arguments See Also Examples

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.

1 2	genomicRegions(chrom, tss, strand, proxUp, proxDown, distal, n = length(chrom), chroms = unique(chrom))

`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)

geneRanges

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)