prepare_genome_builds: Prepare genome builds

In neurogenomics/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

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 April 30, 2024, 3:58 p.m.