genomePartitionList: Create a basic genome partition list of genes, exons,...

In databio/GenomicDistributions: GenomicDistributions: fast analysis of genomic intervals with Bioconductor

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

Description

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.

Usage

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

Details

To be used as a partitionList for calcPartitions.

Value

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

Examples

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

databio/GenomicDistributions documentation built on Nov. 5, 2023, 5:30 p.m.