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",
      bpProportion = FALSE
    )

### Arguments

`query` | GRanges or GRangesList with regions to classify
`partitionList` | an ORDERED (if bpProportion=FALSE) 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. bpProportion=TRUE, the list does not need ordering.
`remainder` | A character vector to assign any query regions that do not overlap with anything in the partitionList. Defaults to "intergenic"
`bpProportion` | logical indicating if overlaps should be calculated based on number of base pairs overlapping with each partition. bpProportion=FALSE does overlaps in priority order, bpProportion=TRUE counts number of overlapping base pairs between query and each partition.

### 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 1.2.0 Index]