CnT_H3K27ac: Example CUT&Tag peak file

In serachoi1230/EpiCompare: Comparison, Benchmarking & QC of Epigenomic Datasets

Example CUT&Tag peak file

Description

Human H3K27ac peak file generated with CUT&Tag using K562 cell-line from Kaya-Okur 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=SRR8383507). Peak calling was performed by Leyla Abbasova using MACS2. The peak file was then imported as an GRanges object. Peaks located on chromosome 1 were subsetted to reduce the dataset size.

Usage

data("CnT_H3K27ac")

Format

An object of class GRanges of length 1670.

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=SRR8383507
# and peaks (BED file) were generated by Leyla Abbasova (Neurogenomics Lab, Imperial College London)
CnT_H3K27ac <- ChIPseeker::readPeakFile("path", as = "GRanges")
CnT_H3K27ac <- CnT_H3K27ac[seqnames(CnT_H3K27ac)== "chr1"]
my_label <- c("name","score","strand","signalValue","pValue","qValue","peak")
colnames(GenomicRanges::mcols(CnT_H3K27ac)) <- my_label
usethis::use_data(CnT_H3K27ac)

serachoi1230/EpiCompare documentation built on Jan. 30, 2024, 11:37 a.m.