ChIPreads: Reads aligned to hg19 from two ChIP-seq experiments

Description Usage Format Details

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, http://members.cbio.mines-paristech.fr/~thocking/chip-seq-chunk-db/

Usage

1
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.


PeakSegDisk documentation built on Sept. 11, 2019, 9:07 a.m.