calcCumulativePartitions: Calculates the cumulative distribution of overlaps between...

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

Calculates the cumulative 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

calcCumulativePartitions(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	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)
calcCumulativePartitions(vistaEnhancers, partitionList)

databio/GenomicDistributions documentation built on April 30, 2024, 4:34 a.m.