calcExpectedPartitions {GenomicDistributions} | R Documentation

## Calculates expected partiton overlap based on contribution of each feature (partition) to genome size. Expected and observed overlaps are then compared.

### Description

Calculates expected partiton overlap based on contribution of each feature (partition) to genome size. Expected and observed overlaps are then compared.

### Usage

    calcExpectedPartitions(
      query,
      partitionList,
      genomeSize = NULL,
      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. However, if bpProportion=TRUE, the list does not need ordering.
`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'?
`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)
    chromSizes = getChromSizes('hg19')
    genomeSize = sum(chromSizes)
    calcExpectedPartitions(vistaEnhancers, partitionList, genomeSize)

[Package GenomicDistributions version 1.2.0 Index]