ChIP-seq analysis with windows

Documentation for package ‘csaw’ version 1.0.7

$-method	readParam class and methods
asDGEList	Statistical wrappers for SummarizedExperiment objects
asDGEList-method	Statistical wrappers for SummarizedExperiment objects
average	Statistical wrappers for SummarizedExperiment objects
average-method	Statistical wrappers for SummarizedExperiment objects
combineTests	Combine statistics across multiple tests
correlateReads	Compute correlation coefficients between reads
csawUsersGuide	View csaw user's guide
detailRanges	Add annotation to ranges
extractReads	Extract reads from a BAM file
getBestTest	Get the best test in a cluster
getPETSizes	Compute fragment lengths for paired-end tags
mergeWindows	Merge windows into clusters
normalize	Statistical wrappers for SummarizedExperiment objects
normalize-method	Statistical wrappers for SummarizedExperiment objects
normalizeCounts	Normalize counts between libraries
readParam	readParam class and methods
readParam-class	readParam class and methods
reform	readParam class and methods
reform-method	readParam class and methods
regionCounts	Count reads overlapping each region
show-method	readParam class and methods
windowCounts	Count reads overlapping each window