calcExpectedPartitionsRef: Calculates the distribution of observed versus expected...

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

Calculates the distribution of observed versus expected overlaps for a query set to a reference assembly

Description

This function is a wrapper for calcExpectedPartitions that uses built-in partitions for a given reference genome assembly.

Usage

calcExpectedPartitionsRef(query, refAssembly, bpProportion = FALSE)

Arguments

query	A GenomicRanges or GenomicRangesList object with query regions
refAssembly	A character vector specifying the reference genome assembly (*e.g.* 'hg19'). This will be used to grab annotation models with getGeneModels, and chromosome sizes withgetChromSizes
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 indicating the number of query region overlaps in several genomic partitions.

Examples

calcExpectedPartitionsRef(vistaEnhancers, "hg19")

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