calcChromBinsRef: Returns the distribution of query over a reference assembly...

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

Returns the distribution of query over a reference assembly Given a query set of elements (a GRanges object) and a reference assembly (*e.g. 'hg38'), this will aggregate and count the distribution of the query elements across bins of the reference genome. This is a helper function to create features for common genomes. It is a wrapper of calcChromBins, which is more general.

Description

Returns the distribution of query over a reference assembly Given a query set of elements (a GRanges object) and a reference assembly (*e.g. 'hg38'), this will aggregate and count the distribution of the query elements across bins of the reference genome. This is a helper function to create features for common genomes. It is a wrapper of calcChromBins, which is more general.

Usage

calcChromBinsRef(query, refAssembly, binCount = 3000)

Arguments

query	A GenomicRanges or GenomicRangesList object with query regions
refAssembly	A character vector that will be used to grab chromosome sizes with getChromSizes
binCount	Number of bins to divide the chromosomes into

Value

A data.table showing the distribution of regions across bins of the reference genome.

Examples

ChromBins = calcChromBinsRef(vistaEnhancers, "hg19")

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