CnR_H3K27ac: Example CUT&Run peak file

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

Example CUT&Run peak file

Description

Human H3K27ac peak file generated with CUT&Run using K562 cell-line from Meers et al., (2019). Human genome build hg19 was used. Raw peak file (.BED) was obtained from GEO (https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8581604). Peak calling was performed by Leyla Abbasova using MACS2. The peak file was then processed into GRanges object. Peaks located on chromosome 1 were subsetted to reduce the dataset size.

Usage

data("CnR_H3K27ac")

Format

An object of class GRanges of length 2707.

Source

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

# sequences were directly downloaded from https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8581604
# and peaks (BED file) were generated by Leyla Abbasova (Neurogenomics Lab, Imperial College London)
CnR_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges")
CnR_H3K27ac <- CnR_H3K27ac[seqnames(CnR_H3K27ac)== "chr1"]
my_label <- c("name","score","strand","signalValue","pValue","qValue","peak")
colnames(GenomicRanges::mcols(CnR_H3K27ac)) <- my_label
usethis::use_data(CnR_H3K27ac, overwrite = TRUE)

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