ChIPQC-data: Example data sets for 'ChIPQC' package, each containing a...

In genialis/ChIPQC: Quality metrics for ChIPseq data

Example data sets for ChIPQC package, each containing a ChIPQCexperiment object, as well as a pre-compiled blacklist for hg19.

Description

The tamoxifen_QC example data set contains a ChIPQCexperiment object named tamoxifen. This data set, based on Ross-Innes et al (2012), includes 11 ER ChIP libraries, and their input controls, divided into tamoxifen responsive and tamoxifen resistant sample groups. Only data for chromosome 18 (chr18) are included.

The example_QCexperiment data set contains a ChIPQCexperiment object named exampleExp. This data set, derived from ENCODE data, includes 6 ChIP libraries. Only data for chromosome 22 (chr22) are included.

blacklist_hg19 data set includes a GRanges object named blacklist_hg19 containing blacklisted regions for the human genome, derived from the UCSC blacklist.

Usage

data(tamoxifen_QC)
data(example_QCexperiment)
data(blacklist_hg19)

Format

tamoxifen_QC: A single ChIPQCexperiment object named tamoxifen is loaded. This object is used for the ChIPQC-package examples and vignette. This object can also be used with the DiffBind package (see related data objects tamoxifen).

example_QCexperiment: A single ChIPQCexperiment object named exampleExp is loaded. This object is used for the ChIPQC-package examples and vignette.

blacklist_hg19: A single GRanges object named blacklist.hg19 that is used by default when processing hg19 data sets.

Source

Ross-Innes, C. S., Stark, R., Teschendorff, A. E., Holmes, K. A., Ali, H. R., Dunning, M. J., Brown, G. D., Gojis, O., Ellis, I. O., Green, A. R., Ali, S., Chin, S.-F., Palmieri, C., Caldas, C., and Carroll, J. S. (2012). Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389-393.

Examples

data(tamoxifen_QC)
tamoxifen
plotRegi(tamoxifen)

data(example_QCexperiment)
exampleExp

data(blacklist_hg19)
blacklist.hg19

genialis/ChIPQC documentation built on May 24, 2022, 5:24 p.m.