extract_epigenome: Extract values for epigenomic features in a given region....

In greymonroe/polymorphology: Functions from Monroe et al 2022

Extract values for epigenomic features in a given region. Used in Monroe et al 2022 Not a very generalizable function as it depends on formatting of datasets.

Description

Extract values for epigenomic features in a given region. Used in Monroe et al 2022 Not a very generalizable function as it depends on formatting of datasets.

Usage

extract_epigenome(
  regions,
  peaks_file,
  meth_file,
  genome_file,
  histone_dir,
  tmp_dir,
  multiBigwigSummary
)

Arguments

regions	data.table object with columns columns chr, start, stop
peaks_file	file with ATACseq peaks
meth_file	file with methylation data
genome_file	reference genome fasta file
histone_dir	directory of files with histone modifications
tmp_dir	directory for temporary files
multiBigwigSummary	system location for multiBigwigSummary function

Value

a data.table annotated with genomic and epigenomic features

greymonroe/polymorphology documentation built on Aug. 6, 2023, 1:33 a.m.