calcCumulativePartitions {GenomicDistributions} | R Documentation

## 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)

[Package GenomicDistributions version 1.2.0 Index]