genomePartitionList {GenomicDistributions} | R Documentation

## 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)

### 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

### 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)

[Package GenomicDistributions version 1.2.0 Index]