Introducing the csaw package
In csaw: ChIP-Seq Analysis with Windows

knitr::opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE)

Introduction

The r Biocpkg("csaw") package is designed for the de novo detection of differentially bound regions from ChIP-seq data. It uses a sliding window approach to count reads across the genome from sorted and indexed BAM files. Each window is then tested for significant differences between libraries, using the methods in the r Biocpkg("edgeR") package. It implements statistical methods for:

normalization of window counts between libraries
independent filtering of uninteresting windows
controlling the false discovery rate across aggregated windows

r Biocpkg("csaw") can be applied to any data set containing multiple conditions with biological replication. While intended for ChIP-seq data, the methods in this package can also be applied to any type of sequencing data where changes in genomic coverage are of interest.

Documentation

The full user's guide is available as part of the online documentation in the r Biocpkg("csawUsersGuide") workflow package. It can be obtained by typing:

library(csaw)
if (interactive()) csawUsersGuide()

In addition, several end-to-end usage examples are provided by the r Biocpkg("chipseqDB") workflow package. This is less comprehensive but more concise than the user's guide.

Documentation for speicific functions is available through the usual R help system, e.g., ?windowCounts. Further questions about the package should be directed to the Bioconductor support site.