peak_info: Summary of Peak Information

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

Summary of Peak Information

Description

This function outputs a table summarizing information on the peak files. Provides the total number of peaks and the percentage of peaks in blacklisted regions.

Usage

peak_info(peaklist, blacklist)

Arguments

peaklist	A named list of peak files as GRanges object. Objects listed using list("name1" = peak, "name2" = peak2).
blacklist	A GRanges object containing blacklisted regions.

Value

A summary table of peak information

Examples

### Load Data ###
data("encode_H3K27ac") # example peakfile GRanges object
data("CnT_H3K27ac") # example peakfile GRanges object
data("hg19_blacklist") # example blacklist GRanges object

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

### Run ###
df <- peak_info(peaklist = peaklist,
                blacklist = hg19_blacklist) 

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