tidy_peakfile: Tidy peakfiles in GRanges

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

Tidy peakfiles in GRanges

Description

This function filters peak files by removing peaks in blacklisted regions and in non-standard chromosomes. It also checks that the input list of peakfiles is named. If no names are provided, default file names will be used.

Usage

tidy_peakfile(peaklist, blacklist)

Arguments

peaklist	A named list of peak files as GRanges object. Objects must be named and listed using list(). e.g. list("name1"=file1, "name2"=file2) If not named, default names are assigned.
blacklist	Peakfile specifying blacklisted regions as GRanges object.

Value

list of GRanges object

Examples

### Load Data ###
data("encode_H3K27ac") # example peakfile GRanges object
data("CnT_H3K27ac") # example peakfile GRanges object
data("hg19_blacklist") # blacklist region for hg19 genome

### Create Named Peaklist ###
peaklist <- list("encode"=encode_H3K27ac, "CnT"=CnT_H3K27ac)

### Run ###
peaklist_tidy <- tidy_peakfile(peaklist = peaklist,
                               blacklist = hg19_blacklist)

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