Given GRanges for genes, and a GRanges for exons, returns a list of GRanges corresponding to various breakdown of the genome, based on the given annotations; it gives you proximal and core promoters, exons, and introns.
genomePartitionList( genesGR, exonsGR, threeUTRGR = NULL, fiveUTRGR = NULL, getCorePromoter = TRUE, getProxPromoter = TRUE, corePromSize = 100, proxPromSize = 2000 )
a GRanges object of gene coordinates
a GRanges object of exons coordinates
a GRanges object of 3' UTRs
a GRanges object of 5' UTRs
option specifying if core promoters should be extracted defeaults to TRUE
option specifying if proximal promoters should be extracted defeaults to TRUE
size of core promoter (in bp) upstrem from TSS default value = 100
size of proximal promoter (in bp) upstrem from TSS default value = 2000
A list of GRanges objects, each corresponding to a partition of the genome. Partitions include proximal and core promoters, exons and introns.
To be used as a partitionList for
partitionList = genomePartitionList(geneModels_hg19$genesGR, geneModels_hg19$exonsGR, geneModels_hg19$threeUTRGR, geneModels_hg19$fiveUTRGR)