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.
data("CnR_H3K27ac")An object of class GRanges of length 2707.
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)