Create a basic genome partition list of genes, exons, introns, UTRs, and intergenic

Source: R/partition-plots.R

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)

Arguments

genesGR

a GRanges object of gene coordinates

exonsGR

a GRanges object of exons coordinates

threeUTRGR

a GRanges object of 3' UTRs

fiveUTRGR

a GRanges object of 5' UTRs

Value

A list of GRanges objects, each corresponding to a partition of the genome. Partitions include proximal and core promoters, exons and introns.

Details

To be used as a partitionList for calcPartitions.

Examples

partitionList = genomePartitionList(geneModels_hg19$genesGR,
                                    geneModels_hg19$exonsGR,
                                    geneModels_hg19$threeUTRGR,
                                    geneModels_hg19$fiveUTRGR)