asDataFrame	asDataFrame
callPeaks	callPeaks
changeSettings	changeSettings
changeSettings,GenomicTiles,character-method	changeSettings
checkSettings	checkSettings
checkSettings,GenomicTiles-method	checkSettings
colData,GenoGAM-method	GenoGAM-methods
computeRegionSignificance	computeRegionSignificance
computeSignificance	computeSignificance
computeSizeFactors	computeSizeFactors
dataRange	dataRange
dataRange,GenomicTiles-method	dataRange
dataRange,GPos-method	dataRange
design,GenoGAM-method	GenoGAM-methods
design,GenoGAMDataSet-method	design
design<-,GenoGAMDataSet,ANY-method	design
filterData	filterData
GenoGAM	GenoGAM
genogam	fitGenoGAM
GenoGAM-class	GenoGAM-class
GenoGAM-methods	GenoGAM-methods
GenoGAMDataSet	GenoGAMDataSet
GenoGAMDataSet-class	GenoGAMDataSet-class
GenoGAMDataSetToDataFrame	GenoGAMDataSetToDataFrame
GenoGAMSettings	GenoGAMSettings
GenoGAMSettings-class	GenoGAMSettings-class
GenomicTiles	GenomicTiles
GenomicTiles-class	GenomicTiles-class
getChromosomes	tileSettings-elements
getChromosomes,GenomicTiles-method	tileSettings-elements
getChunkIndex	getChunkIndex
getChunkIndex,GenomicTiles-method	getChunkIndex
getChunkSize	tileSettings-elements
getChunkSize,GenomicTiles-method	tileSettings-elements
getCoordinates	getCoordinates
getCoordinates,GenomicTiles-method	getCoordinates
getFits	GenoGAM-methods
getFits,GenoGAM-method	GenoGAM-methods
getIndex	getIndex
getIndex,GenomicTiles-method	getIndex
getIndexCoordinates	getIndexCoordinates
getIndexCoordinates,GenomicTiles-method	getIndexCoordinates
getOverhangSize	tileSettings-elements
getOverhangSize,GenomicTiles-method	tileSettings-elements
getTile	getTile
getTile,GenomicTiles-method	getTile
getTileNumber	tileSettings-elements
getTileNumber,GenomicTiles-method	tileSettings-elements
getTileSize	tileSettings-elements
getTileSize,GenomicTiles-method	tileSettings-elements
IQR,GenomicTiles-method	GenomicTiles-metrics
mad,GenomicTiles-method	GenomicTiles-metrics
makeTestGenoGAM	makeTestGenoGAM
makeTestGenoGAMDataSet	makeTestGenoGAMDataSet
makeTestGenomicTiles	makeTestGenomicTiles
mean,GenomicTiles-method	GenomicTiles-metrics
median,GenomicTiles-method	GenomicTiles-metrics
plot.GenoGAM	plot.GenoGAM
qualityCheck	qualityCheck
rowRanges,GenoGAM-method	GenoGAM-methods
sd,GenomicTiles-method	GenomicTiles-metrics
sizeFactors,GenoGAMDataSet-method	sizeFactors
sizeFactors<-,GenoGAMDataSet,ANY-method	sizeFactors
subset,GenoGAM-method	subset-GenoGAM-method
subset,GenoGAMDataSet-method	subset-GenoGAMDataSet-method
subset,GenomicTiles-method	subset-GenomicTiles-method
subsetByOverlaps,GenoGAM,ANY-method	subsetByOverlaps-GenoGAM-ANY-method
subsetByOverlaps,GenoGAMDataSet,GRanges-method	subsetByOverlaps-GenoGAMDataSet-GRanges-method
subsetByOverlaps,GenomicTiles,GRanges-method	subsetByOverlaps-GenomicTiles-GRanges-method
Summary,GenomicTiles-method	GenomicTiles-metrics
tileSettings	tileSettings
tileSettings,GenomicTiles-method	tileSettings
untile	untile
untile,GenomicTiles-method	untile
var,GenomicTiles,ANY-method	GenomicTiles-metrics
view	GenomicTiles-view
view,GenoGAM-method	GenoGAM-view
view,GenomicTiles-method	GenomicTiles-view
writeToBEDFile	writeToBEDFile
[,GenoGAMDataSet,GRanges,ANY,ANY-method	GenoGAMDataSet-brackets
[,GenomicTiles,GRanges,ANY,ANY-method	GenomicTiles-brackets
[[,GenomicTiles,numeric,ANY-method	GenomicTiles-brackets
