calcExpectedPartitions: Calculates expected partiton overlap based on contribution of...

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

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.The data.frame also contains Chi-square p-values calculated for observed/expected overlaps on each individual partition.

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)

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