ChIPreads {PeakSegDisk}

Reads aligned to hg19 from two ChIP-seq experiments

Description

These data are raw aligned reads which have been mapped to the human genome, hg19. One is sample ID McGill0004, experiment H3K36me3, chr9, chunk H3K36me3_AM_immune/8. The other is sample ID McGill0002, experiment H3K4me3, chr2, chunk H3K4me3_PGP_immune/7. The chunk ID numbers refer to parts of the McGill benchmark data set, https://rcdata.nau.edu/genomic-ml/chip-seq-chunk-db/

Usage

data("ChIPreads")

Format

A data frame with 40396 observations on the following 4 variables.

experiment

either H3K36me3 or H3K4me3

chrom

either chr9 or chr2

chromStart

0-based start position of read

chromEnd

1-based end position of read

count

number of times a read occured with the given chromStart/end in this sample/experiment

Details

Peak detection algorithm are typically run on a sequence of non-negative integer count data, one data point for each genomic position. These data are useful for proving that peak detection methods are robust to different sequences: (1) spatially correlated, non-independent aligned read coverage; (2) un-correlated, independent representations such as first or last read.