ChIP-seq analysis with windows


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Documentation for package ‘csaw’ version 1.0.7

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$-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