ChIP-seq analysis with windows


[Up] [Top]

Documentation for package ‘csaw’ version 1.4.1

Help Pages

$-method readParam class and methods
asDGEList Statistical wrappers for RangedSummarizedExperiment objects
asDGEList-method Statistical wrappers for RangedSummarizedExperiment objects
checkBimodality Check bimodality of regions
checkList Get or modify readParam lists
clusterFDR Compute the cluster-level FDR
combineOverlaps Compute overlap statistics
combineTests Combine statistics across multiple tests
consolidateSizes Consolidate window sizes
correlateReads Compute correlation coefficients between reads
csaw View csaw user's guide
csawUsersGuide View csaw user's guide
detailRanges Add annotation to ranges
dumpPE Dump paired-end data to file
extractReads Extract reads from a BAM file
filterWindows Filtering methods for RangedSummarizedExperiment objects
findMaxima Find local maxima
getBestOverlaps Compute overlap statistics
getBestTest Get the best test in a cluster
getPESizes Compute fragment lengths for paired-end tags
getWidths Get region widths
makeExtVector Make an extVector object
maximizeCcf Find the delay at the maximal CCF
mergeWindows Merge windows into clusters
normalize Statistical wrappers for RangedSummarizedExperiment objects
normalize-method Statistical wrappers for RangedSummarizedExperiment objects
normOffsets Normalize counts between libraries
normOffsets-method Statistical wrappers for RangedSummarizedExperiment objects
normOffsets-method Normalize counts between libraries
profileSites Profile binding sites
readParam readParam class and methods
readParam-class readParam class and methods
reform readParam class and methods
reform-method readParam class and methods
reformList Get or modify readParam lists
regionCounts Count reads overlapping each region
scaledAverage Scaled average abundance
show-method readParam class and methods
strandedCounts Get strand-specific counts
summitOverlaps Compute overlap statistics
upweightSummit Upweight summits
windowCounts Count reads overlapping each window
wwhm Window width at half maximum
[.extVector Make an extVector object