$,readParam-method	readParam
asDGEList	SEmethods
asDGEList,SummarizedExperiment-method	SEmethods
calculateCPM	calculateCPM
checkBimodality	checkBimodality
cluster-direction	cluster-direction
clusterFDR	clusterFDR
clusterWindows	clusterWindows
clusterWindowsList	clusterWindowsList
combineOverlaps	overlapStats
combineTests	combineTests
consolidateOverlaps	defunct
consolidateTests	defunct
consolidateWindows	defunct
controlClusterFDR	clusterFDR
correlateReads	correlateReads
csaw	csawUsersGuide
csawUsersGuide	csawUsersGuide
defunct	defunct
detailRanges	detailRanges
empiricalFDR	empiricalFDR
empiricalOverlaps	overlapStats
extractReads	extractReads
filterWindows	defunct
filterWindowsControl	filterWindows
filterWindowsGlobal	filterWindows
filterWindowsLocal	filterWindows
filterWindowsProportion	filterWindows
findMaxima	findMaxima
findOverlapsList	mergeWindowsList
getBestOverlaps	overlapStats
getBestTest	getBestTest
getPESizes	getPESizes
getWidths	getWidths
maximizeCcf	maximizeCcf
mergeResults	mergeResults
mergeResultsList	mergeResultsList
mergeWindows	mergeWindows
mergeWindowsList	mergeWindowsList
minimalTests	minimalTests
mixedClusters	mixedTests
mixedOverlaps	overlapStats
mixedTests	mixedTests
normFactors	normFactors
normOffsets	normOffsets
overlapResults	mergeResults
overlapResultsList	mergeResultsList
overlapStats	overlapStats
profileSites	profileSites
readParam	readParam
readParam-class	readParam
reform	readParam
reform,readParam-method	readParam
regionCounts	regionCounts
scaleControlFilter	filterWindows
scaledAverage	scaledAverage
show,readParam-method	readParam
strandedCounts	strandedCounts
summitOverlaps	overlapStats
upweightSummit	upweightSummit
windowCounts	windowCounts
wwhm	wwhm
