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

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
)

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

getCorePromoter

option specifying if core promoters should be extracted defeaults to TRUE

getProxPromoter

option specifying if proximal promoters should be extracted defeaults to TRUE

corePromSize

size of core promoter (in bp) upstrem from TSS default value = 100

proxPromSize

size of proximal promoter (in bp) upstrem from TSS default value = 2000

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)