DF_H3K4me3: Example of a coverage matrix using the ChIP-seq data for the H3K4me3 histone modification experiment

Description

A coverage matrix calculated using the H3K4me3 ChIP-seq data from the K562 cell line. This matrix was computed using only the reads aligned into the Human chromosome 19

Usage

data(DF_H3K4me3)

Arguments

Format

matrix with the normalized (read per million) coverages for the genomic interval corresponding to the gene body of a certain set of genes

Source

H3K4me3 ChIP-seq data set for the K562 cell line from the HudsonAlpha Institute that was used as a test case in the Nature protocol named: Identifying ChIP-seq enrichment using MACS. Feng J, Liu T, Qin B, Zhang Y, Liu XS. Nat Protoc. 2012 Sep;7(9):1728-40.

Details

This matrix was obtained by running the CoverageView function named cov.matrix and setting the no_windows parameter to 100, the normalization parameter to "rpm" and the offset parameter to 10. The BED format coordinate file was passed to the function through the coordfile argument and contained the genomic coordinates of a set of genes for which the region starting 2500 nucleotides before the transcription start site (TSS) and ending in the transcription end site (TES) contains at least one enrichment peak identified by MACS using the ChIP-seq data. All peaks, regardless its false discovery rate, were considered. For illustrative purposes only the genes located in the chr19 were analyzed.

References

Zhang et al. Model-based Analysis of ChIP-Seq (MACS). Genome Biol (2008) vol. 9 (9) pp. R137".