calcExpectedPartitionsRef {GenomicDistributions}R Documentation

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)

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 chromosome sizes with getTSSs.

Value

A data.frame indicating the number of query region overlaps in several genomic partitions.

Examples

calcExpectedPartitionsRef(vistaEnhancers, "hg19")

[Package GenomicDistributions version 1.0.0 Index]