ChIP-Seq Analysis with Windows

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Documentation for package ‘csaw’ version 1.42.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

$-method	readParam class and methods
asDGEList	SummarizedExperiment to DGEList
asDGEList-method	SummarizedExperiment to DGEList
calculateCPM	Calculate CPM
checkBimodality	Check bimodality of regions
cluster-direction	Reporting cluster-level direction in 'csaw'
clusterFDR	Compute the cluster-level FDR
clusterWindows	Cluster DB windows into clusters
clusterWindowsList	Consolidate DB clusters
combineOverlaps	Combine statistics for overlap-based clusters
combineTests	Combine statistics across multiple tests
consolidateOverlaps	Defunct functions
consolidateTests	Defunct functions
consolidateWindows	Defunct functions
controlClusterFDR	Compute the cluster-level FDR
correlateReads	Compute correlation coefficients between reads
csaw	View csaw user's guide
csawUsersGuide	View csaw user's guide
defunct	Defunct functions
detailRanges	Add annotation to ranges
empiricalFDR	Control the empirical FDR
empiricalOverlaps	Combine statistics for overlap-based clusters
extractReads	Extract reads from a BAM file
filterWindows	Defunct functions
filterWindowsControl	Filtering methods for RangedSummarizedExperiment objects
filterWindowsGlobal	Filtering methods for RangedSummarizedExperiment objects
filterWindowsLocal	Filtering methods for RangedSummarizedExperiment objects
filterWindowsProportion	Filtering methods for RangedSummarizedExperiment objects
findMaxima	Find local maxima
findOverlapsList	Consolidate window sizes
getBestOverlaps	Combine statistics for overlap-based clusters
getBestTest	Get the best test in a cluster
getPESizes	Compute fragment lengths for paired-end tags
getWidths	Get region widths
maximizeCcf	Find the delay at the maximal CCF
mergeResults	Wrappers to get region-level results
mergeResultsList	Wrappers to combine multiple analyses
mergeWindows	Merge windows into clusters
mergeWindowsList	Consolidate window sizes
minimalTests	Require rejection of a minimal number of tests
mixedClusters	Tests for mixed DB clusters
mixedOverlaps	Combine statistics for overlap-based clusters
mixedTests	Tests for mixed DB clusters
normFactors	Scaling normalization across libraries
normOffsets	Normalize trended biases across libraries
overlapResults	Wrappers to get region-level results
overlapResultsList	Wrappers to combine multiple analyses
overlapStats	Combine statistics for overlap-based clusters
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
regionCounts	Count reads overlapping each region
scaleControlFilter	Filtering methods for RangedSummarizedExperiment objects
scaledAverage	Scaled average abundance
show-method	readParam class and methods
strandedCounts	Get strand-specific counts
summitOverlaps	Combine statistics for overlap-based clusters
upweightSummit	Upweight summits
windowCounts	Count reads overlapping each window
wwhm	Window width at half maximum