ChIPQC-package {ChIPQC} | R Documentation

## ChIPQC - Quality metrics for ChIPseq data

### Description

ChIPQC analyzes aligned reads (in .bam format) for ChIP-seq samples and their associated controls, computing a variety of quality control metrics and statistics, and providing reporting and plotting functions to enable assessment of experimental data for further analysis.

### Details

Package: | ChIPQC
Type: | Package
Version: | 0.1
Date: | 2014-03-01
License: | GPL3

`ChIPQC` primarily uses two object classes: `ChIPQCsample`, which encapsulates the information about individual samples, and `ChIPQCexperiment`, which encapsulates information about larger ChIP-seq experiments (consisting of a number of samples). The primary entry point is the constructor function `ChIPQC`, which takes a description of an entire experiment, constructs objects for all the samples, and computes the quality metrics.

### Author(s)

Tom Carroll and Rory Stark

Maintainers: Tom Carroll <tc.infomatics@gmail.com> and Rory Stark <rory.stark@cruk.cam.ac.uk>

### References

Frontiers?

### See Also

`ChIPQC` is designed to work closely with the `DiffBind` package, which provides functionality for analyzing ChIP-seq experiments, including performing differential binding analysis to identify significantly differentially bound peaks.

[Package ChIPQC version 1.22.0 Index]