GenoGAM-package	GenoGAM
asCoordinates	asCoordinates
assay,GenoGAM,missing-method	GenoGAM-class
assay,GenoGAMDataSetList,ANY-method	GenoGAMDataSetList-class
assay,GenoGAMList,missing-method	GenoGAMList-class
assays,GenoGAMDataSetList-method	GenoGAMDataSetList-class
assays,GenoGAMList-method	GenoGAMList-class
callPeaks	callPeaks
colData	GenoGAM-class
colData,GenoGAM-method	GenoGAM-class
colData,GenoGAMDataSetList-method	GenoGAMDataSetList-class
colData,GenoGAMList-method	GenoGAMList-class
colnames	GenoGAM-class
colnames,GenoGAM-method	GenoGAM-class
colnames,GenoGAMDataSetList-method	GenoGAMDataSetList-class
colnames,GenoGAMList-method	GenoGAMList-class
computeRegionSignificance	computeRegionSignificance
computeSignificance	computeSignificance
computeSizeFactors	computeSizeFactors
Coordinates	Coordinates-class
Coordinates-class	Coordinates-class
dataRange	GenoGAMDataSet-class
dataRange,GenoGAMDataSet-method	GenoGAMDataSet-class
dataRange,GenoGAMDataSetList-method	GenoGAMDataSetList-class
design,GenoGAM-method	GenoGAM-class
design,GenoGAMDataSet-method	GenoGAMDataSet-class
design,GenoGAMDataSetList-method	GenoGAMDataSetList-class
design,GenoGAMList-method	GenoGAMList-class
design<-,GenoGAMDataSet,ANY-method	GenoGAMDataSet-class
design<-,GenoGAMDataSetList,ANY-method	GenoGAMDataSetList-class
dim,GenoGAMDataSetList-method	GenoGAMDataSetList-class
dim,GenoGAMList-method	GenoGAMList-class
dimnames	GenoGAM-class
dimnames,GenoGAM-method	GenoGAM-class
dimnames,GenoGAMList-method	GenoGAMList-class
end,Coordinates-method	Coordinates-class
end<-,Coordinates-method	Coordinates-class
fits	GenoGAM-class
fits,GenoGAM-method	GenoGAM-class
fits,GenoGAMList-method	GenoGAMList-class
GenoGAM	GenoGAM-class
GenoGAM	GenoGAM
genogam	fitGenoGAM
GenoGAM-class	GenoGAM-class
GenoGAMDataSet	GenoGAMDataSet-class
GenoGAMDataSet-class	GenoGAMDataSet-class
GenoGAMDataSetList	GenoGAMDataSetList-class
GenoGAMDataSetList-class	GenoGAMDataSetList-class
GenoGAMFamily-class	GenoGAMFamily-class
GenoGAMList	GenoGAMList-class
GenoGAMList-class	GenoGAMList-class
GenoGAMSettings	GenoGAMSettings-class
GenoGAMSettings-class	GenoGAMSettings-class
getChromosomes	GenoGAMDataSet-class
getChromosomes,GenoGAMDataSet-method	GenoGAMDataSet-class
getChromosomes,GenoGAMDataSetList-method	GenoGAMDataSetList-class
getChunkSize	GenoGAMDataSet-class
getChunkSize,GenoGAMDataSet-method	GenoGAMDataSet-class
getChunkSize,GenoGAMDataSetList-method	GenoGAMDataSetList-class
getChunkSize<-	GenoGAMDataSet-class
getChunkSize<-,GenoGAMDataSet,numeric-method	GenoGAMDataSet-class
getChunkSize<-,GenoGAMDataSetList,numeric-method	GenoGAMDataSetList-class
getCoefs	GenoGAM-class
getCoefs,GenoGAM-method	GenoGAM-class
getCoefs,GenoGAMList-method	GenoGAMList-class
getCountMatrix,GenoGAMDataSet-method	GenoGAMDataSet-class
getCountMatrix,GenoGAMDataSetList-method	GenoGAMDataSetList-class
getFamily	GenoGAM-class
getFamily,GenoGAM-method	GenoGAM-class
getFamily,GenoGAMList-method	GenoGAMList-class
getIndex	GenoGAMDataSet-class
getIndex,GenoGAMDataSet-method	GenoGAMDataSet-class
getIndex,GenoGAMDataSetList-method	GenoGAMDataSetList-class
getKnots	GenoGAM-class
getKnots,GenoGAM-method	GenoGAM-class
getKnots,GenoGAMList-method	GenoGAMList-class
getOverhangSize	GenoGAMDataSet-class
getOverhangSize,GenoGAMDataSet-method	GenoGAMDataSet-class
getOverhangSize,GenoGAMDataSetList-method	GenoGAMDataSetList-class
getOverhangSize<-	GenoGAMDataSet-class
getOverhangSize<-,GenoGAMDataSet,numeric-method	GenoGAMDataSet-class
getOverhangSize<-,GenoGAMDataSetList,numeric-method	GenoGAMDataSetList-class
getParams	GenoGAM-class
getParams,GenoGAM-method	GenoGAM-class
getParams,GenoGAMList-method	GenoGAMList-class
getSettings	GenoGAM-class
getSettings,GenoGAM-method	GenoGAM-class
getSettings,GenoGAMList-method	GenoGAMList-class
getTileNumber	GenoGAMDataSet-class
getTileNumber,GenoGAMDataSet-method	GenoGAMDataSet-class
getTileNumber,GenoGAMDataSetList-method	GenoGAMDataSetList-class
getTileNumber<-	GenoGAMDataSet-class
getTileNumber<-,GenoGAMDataSet,numeric-method	GenoGAMDataSet-class
getTileNumber<-,GenoGAMDataSetList,numeric-method	GenoGAMDataSetList-class
getTileSize	GenoGAMDataSet-class
getTileSize,GenoGAMDataSet-method	GenoGAMDataSet-class
getTileSize,GenoGAMDataSetList-method	GenoGAMDataSetList-class
getTileSize<-	GenoGAMDataSet-class
getTileSize<-,GenoGAMDataSet,numeric-method	GenoGAMDataSet-class
getTileSize<-,GenoGAMDataSetList,numeric-method	GenoGAMDataSetList-class
IQR,GenoGAMDataSet-method	GenoGAMDataSet-metrics
IQR,GenoGAMDataSetList-method	GenoGAMDataSet-metrics
is.HDF5,GenoGAM-method	GenoGAM-class
is.HDF5,GenoGAMDataSet-method	GenoGAMDataSet-class
is.HDF5,GenoGAMDataSetList-method	GenoGAMDataSetList-class
is.HDF5,GenoGAMList-method	GenoGAMList-class
length,Coordinates-method	Coordinates-class
length,GenoGAMDataSetList-method	GenoGAMDataSetList-class
length,GenoGAMList-method	GenoGAMList-class
mad,GenoGAMDataSet-method	GenoGAMDataSet-metrics
mad,GenoGAMDataSetList-method	GenoGAMDataSet-metrics
makeTestGenoGAM	makeTestGenoGAM
makeTestGenoGAMDataSet	makeTestGenoGAMDataSet
makeTestGenoGAMDataSetList	makeTestGenoGAMDataSetList
makeTestGenoGAMList	makeTestGenoGAMList
mean,GenoGAMDataSet-method	GenoGAMDataSet-metrics
mean,GenoGAMDataSetList-method	GenoGAMDataSet-metrics
median,GenoGAMDataSet-method	GenoGAMDataSet-metrics
median,GenoGAMDataSetList-method	GenoGAMDataSet-metrics
ncol,Coordinates-method	Coordinates-class
nrow,Coordinates-method	Coordinates-class
plotGenoGAM	plotGenoGAM
pvalue,GenoGAM-method	GenoGAM-class
pvalue,GenoGAMList-method	GenoGAMList-class
readData	readData
rowRanges,GenoGAMDataSetList-method	GenoGAMDataSetList-class
rowRanges,GenoGAMList-method	GenoGAMList-class
sd,GenoGAMDataSet-method	GenoGAMDataSet-metrics
sd,GenoGAMDataSetList-method	GenoGAMDataSet-metrics
se	GenoGAM-class
se,GenoGAM-method	GenoGAM-class
se,GenoGAMList-method	GenoGAMList-class
seqlengths,GenoGAMDataSetList-method	GenoGAMDataSetList-class
seqlengths,GenoGAMList-method	GenoGAMList-class
seqlevels,GenoGAMDataSetList-method	GenoGAMDataSetList-class
seqlevels,GenoGAMList-method	GenoGAMList-class
seqlevelsInUse,GenoGAMDataSetList-method	GenoGAMDataSetList-class
seqlevelsInUse,GenoGAMList-method	GenoGAMList-class
sizeFactors,GenoGAM-method	GenoGAM-class
sizeFactors,GenoGAMDataSet-method	GenoGAMDataSet-class
sizeFactors,GenoGAMDataSetList-method	GenoGAMDataSetList-class
sizeFactors,GenoGAMList-method	GenoGAMList-class
sizeFactors<-,GenoGAMDataSet,ANY-method	GenoGAMDataSet-class
sizeFactors<-,GenoGAMDataSetList,ANY-method	GenoGAMDataSetList-class
start,Coordinates-method	Coordinates-class
start<-,Coordinates-method	Coordinates-class
subset,GenoGAMDataSet-method	GenoGAMDataSet-subsetting
subset,GenoGAMDataSetList-method	GenoGAMDataSetList-subsetting
subset,GenoGAMList-method	GenoGAMList-subsetting
subsetByOverlaps,GenoGAMDataSet,GRanges-method	GenoGAMDataSet-subsetting
subsetByOverlaps,GenoGAMDataSetList,GRanges-method	GenoGAMDataSetList-subsetting
subsetByOverlaps,GenoGAMList,GRanges-method	GenoGAMList-subsetting
Summary,GenoGAMDataSet-method	GenoGAMDataSet-metrics
Summary,GenoGAMDataSetList-method	GenoGAMDataSetList-metrics
tileSettings	GenoGAMDataSet-class
tileSettings,GenoGAMDataSet-method	GenoGAMDataSet-class
tileSettings,GenoGAMDataSetList-method	GenoGAMDataSetList-class
var,GenoGAMDataSet,ANY-method	GenoGAMDataSet-metrics
var,GenoGAMDataSetList,ANY-method	GenoGAMDataSet-metrics
width,Coordinates-method	Coordinates-class
writeToBEDFile	writeToBEDFile
[,GenoGAM,GRanges,ANY,ANY-method	GenoGAM-class
[,GenoGAMDataSet,GRanges,ANY,ANY-method	GenoGAMDataSet-subsetting
[,GenoGAMDataSetList,GRanges,ANY,ANY-method	GenoGAMDataSetList-subsetting
[,GenoGAMList,GRanges,ANY,ANY-method	GenoGAMList-subsetting
