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)
a GRanges object of gene coordinates
a GRanges object of exons coordinates
a GRanges object of 3' UTRs
a GRanges object of 5' UTRs
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)