encode_H3K27ac: Example ChIP-seq peak file

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

Example ChIP-seq peak file

Description

Human H3K27ac peak file generated with ChIP-seq using K562 cell-line. Human genome build hg19 was used. The peak file (.BED) was obtained from ENCODE project (https://www.encodeproject.org/files/ENCFF044JNJ/). The BED file was then imported as an GRanges object. Peaks located on chromosome 1 were subsetted to reduce the dataset size.

Usage

data("encode_H3K27ac")

Format

An object of class GRanges of length 5142.

Source

The code to prepare the .Rda file from the raw peak file is:

# dataset was directly downloaded from
# https://www.encodeproject.org/files/ENCFF044JNJ/ encode_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges")
encode_H3K27ac <- encode_H3K27ac[seqnames(encode_H3K27ac) == "chr1"]
my_label <- c("name","score","strand","signalValue","pValue","qValue","peak")
colnames(GenomicRanges::mcols(encode_H3K27ac)) <- my_label
usethis::use_data(encode_H3K27ac, overwrite = TRUE)

neurogenomics/EpiCompare documentation built on April 30, 2024, 3:58 p.m.