prepare_genome_builds: Prepare genome builds

View source: R/prepare_genome_builds.R

prepare_genome_buildsR Documentation

Prepare genome builds

Description

Parse the genome_build argument into peaklist_build and reference_build.

Usage

prepare_genome_builds(genome_build, blacklist = NULL)

Arguments

genome_build

A named list indicating the human genome build used to generate each of the following inputs:

  • "peakfiles" : Genome build for the peakfiles input. Assumes genome build is the same for each element in the peakfiles list.

  • "reference" : Genome build for the reference input.

  • "blacklist" : Genome build for the blacklist input.

Example input list:
genome_build = list(peakfiles="hg38", reference="hg19", blacklist="hg19")

Alternatively, you can supply a single character string instead of a list. This should only be done in situations where all three inputs (peakfiles, reference, blacklist) are of the same genome build. For example:
genome_build = "hg19"

blacklist

A GRanges object containing blacklisted genomic regions. Blacklists included in EpiCompare are:

  • NULL (default): Automatically selects the appropriate blacklist based on the genome_build_output argument.

  • "hg19_blacklist": Regions of hg19 genome that have anomalous and/or unstructured signals. hg19_blacklist

  • "hg38_blacklist": Regions of hg38 genome that have anomalous and/or unstructured signals. hg38_blacklist

  • "mm10_blacklist": Regions of mm10 genome that have anomalous and/or unstructured signals. mm10_blacklist

  • "mm9_blacklist": Blacklisted regions of mm10 genome that have been lifted over from mm10_blacklist. mm9_blacklist

  • <user_input>: A custom user-provided blacklist in GRanges format.

Value

Named list.


neurogenomics/EpiCompare documentation built on Oct. 18, 2024, 11:04 p.m.