calcExpectedPartitions {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

calcExpectedPartitions(
  query,
  partitionList,
  genomeSize = NULL,
  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.

genomeSize

The number of bases in the query genome. In other words, the sum of all chromosome sizes.

remainder

Which partition do you want to account for 'everything else'?

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)
chromSizes = getChromSizes('hg19')
genomeSize = sum(chromSizes)
calcExpectedPartitions(vistaEnhancers, partitionList, genomeSize)

[Package GenomicDistributions version 1.0.0 Index]