calcPartitionsRef: Calculates the distribution of overlaps for a query set to a...

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

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

Description

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

Usage

calcPartitionsRef(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
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

calcPartitionsRef(vistaEnhancers, "hg19")

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