calcPartitions {GenomicDistributions}R Documentation

Calculates the distribution of overlaps between query and arbitrary genomic partitions

Description

Takes a GRanges object, then assigns each element to a partition from the provided partitionList, and then tallies the number of regions assigned to each partition. A typical example of partitions is promoter, exon, intron, etc; this function will yield the number of each for a query GRanges object There will be a priority order to these, to account for regions that may overlap multiple genomic partitions.

Usage

calcPartitions(query, partitionList, remainder = "intergenic")

Arguments

query

GRanges or GRangesList with regions to classify

partitionList

an ORDERED and NAMED list of genomic partitions GRanges. This list must be in priority order; the input will be assigned to the first partition it overlaps

remainder

A character vector to assign any query regions that do not overlap with anything in the partitionList. Defaults to "intergenic"

Value

A data.frame assigning each element of a GRanges object to a partition from a previously provided partitionList.

Examples

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

[Package GenomicDistributions version 1.0.0 Index]