GenoGAM
A GAM based framework for analysis of ChIP-Seq data

Package index
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Vignettes
Functions
380
Source code
40
Man pages
26
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GenoGAM: A GAM based framework for analysis of ChIP-Seq data
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API

API for GenoGAM
A GAM based framework for analysis of ChIP-Seq data

Global functions
.GenoGAMDataSetFromConfig Source code
.GenoGAMDataSetFromHDF5 Source code
.GenoGAMDataSetFromSE Source code
.GenoGAMFromHDF5 Source code
.GenoGAMListFromHDF5 Source code
.Hupdate Source code
.MetricsFun Source code
.MetricsFunGGD Source code
.MetricsFunGGDL Source code
.MetricsFunHDF5 Source code
.MetricsFunSimple Source code
.absRanges Source code
.blockMatrixFromDesignMatrix Source code
.block_APPLY Source code
.bspline Source code
.buildDesignMatrix Source code
.buildIMatrix Source code
.buildResponseVector Source code
.buildSMatrix Source code
.callBroadPeaks Source code
.callBroadPeaks_default Source code
.callBroadPeaks_hdf5 Source code
.callBroadPeaks_split Source code
.callBroadPeaks_split_hdf5 Source code
.callNarrowPeaks Source code
.callNarrowPeaks_default Source code
.callNarrowPeaks_hdf5 Source code
.callNarrowPeaks_split Source code
.callNarrowPeaks_split_hdf5 Source code
.centerFragments Source code
.check Source code Source code
.checkChromosomes Source code
.checkChunkSize Source code
.checkEqualityOfTiles Source code
.checkFormulaVariables Source code
.checkGenoGAMDataSet Source code
.checkNumberOfTiles Source code
.checkSettings Source code
.checkTileRanges Source code
.checkTileSize Source code
.computeBackground Source code
.computeBackground_default Source code
.computeBackground_hdf5 Source code
.computeBackground_split Source code
.computeBackground_split_hdf5 Source code
.computeDirection Source code
.compute_SE Source code
.compute_hessian Source code
.countFragments Source code
.createH5DF Source code
.createH5Dataset Source code
.createH5File Source code
.deseq Source code
.doCrossValidation Source code
.end_Queue Source code
.estimateParams Source code
.extractGR Source code
.fillParameters Source code
.findPeaks Source code
.findPeaks_hdf5 Source code
.findValleys Source code
.findValleys_hdf5 Source code
.fitGenoGAM Source code
.generateKnotPositions Source code
.getChunkCoords Source code
.getCoordinates Source code
.getCoordinatesGGD Source code
.getCoordinatesGGDL Source code
.getDesignFromFormula Source code
.getFits Source code
.getFragments Source code
.getIdentifier Source code
.getListedCoordinates Source code
.getPairedCenters Source code
.getVars Source code
.get_chunkdim Source code
.get_pvals_default Source code
.get_pvals_split Source code
.get_seed Source code
.hdf5_block_pval Source code
.init_Queue Source code
.initializeHDF5Params Source code
.initiate Source code
.invertHessian Source code
.irls_nb Source code
.lbfgs Source code
.leaveOutConsecutiveIntervals Source code
.linesearch Source code
.loglik Source code
.makeBy Source code
.makeFilename Source code
.makeGrid Source code
.makeNames Source code
.makeSumMatrix Source code
.makeTiles Source code
.median_hdf5 Source code
.mnames Source code
.mu0_split Source code
.mu0_split_hdf5 Source code
.nbeta Source code
.newton Source code
.nfun Source code
.normalize Source code
.normalizeConfig Source code
.placeKnots Source code
.processCountChunks Source code
.pvals Source code
.pvals_default Source code
.pvals_hdf5 Source code
.pvals_hdf5_split Source code
.pvals_split Source code
.queue Source code
.readBAM Source code
.readRawData Source code
.rowRangesFromList Source code
.setOptimalChunkSize Source code
.shorth_hdf5 Source code
.showGenoGAM Source code Source code
.showGenoGAMDataSet Source code
.showGenoGAMSettings Source code
.subsetByCoords Source code
.subsetByOverlapsGGD Source code
.subsetByOverlapsGGDL Source code
.subsetByOverlapsGGL Source code
.subsetIndex Source code
.subsetIndexGGD Source code
.subsetIndexGGDL Source code
.transformResults Source code
.unqueue Source code
.validateBAMParamsType Source code
.validateBetaType Source code
.validateChromosomes Source code
.validateCoefsType Source code
.validateControlType Source code
.validateCoordinates Source code
.validateCountMatrixType Source code
.validateDataControlType Source code
.validateDataType Source code
.validateDesignMatrixType Source code
.validateDesignType Source code Source code
.validateEstimControlType Source code
.validateFactorialDesign Source code
.validateFamilyType Source code Source code
.validateFitsType Source code
.validateFormulaType Source code
.validateGGDLChromosomes Source code
.validateGGKnotsType Source code
.validateGGSDesignType Source code
.validateGGSKnotsType Source code
.validateGenoGAM Source code
.validateGenoGAMDataSet Source code
.validateGenoGAMDataSetList Source code
.validateGenoGAMFamily Source code
.validateGenoGAMList Source code
.validateGenoGAMSettings Source code
.validateGenoGAMSetup Source code
.validateGradient Source code
.validateH5Type Source code
.validateHDF5ControlType Source code
.validateHessian Source code
.validateIDType Source code
.validateIndexType Source code
.validateLogLik Source code
.validateName Source code
.validateOffsetType Source code
.validateOptimControlType Source code
.validateOptimMethodType Source code
.validateParamsElements Source code
.validateParamsType Source code Source code
.validatePenaltyMatrixType Source code
.validateResponseType Source code
.validateSEType Source code
.validateSFType Source code Source code
.validateSettingsType Source code Source code
.var0_hdf5 Source code
.var0_split Source code
.var0_split_hdf5 Source code
.writeToHDF5 Source code
Coordinates Man page Source code
Coordinates-class Man page
GenoGAM Man page Man page Source code
GenoGAM-class Man page
GenoGAM-package Man page
GenoGAMDataSet Man page Source code
GenoGAMDataSet-class Man page
GenoGAMDataSetList Man page Source code
GenoGAMDataSetList-class Man page
GenoGAMFamily Source code
GenoGAMFamily-class Man page
GenoGAMList Man page Source code
GenoGAMList-class Man page
GenoGAMSettings Man page Source code
GenoGAMSettings-class Man page
GenoGAMSetup Source code
IQR,GenoGAMDataSet-method Man page
IQR,GenoGAMDataSetList-method Man page
Summary,GenoGAMDataSet-method Man page
Summary,GenoGAMDataSetList-method Man page
[,GenoGAM,GRanges,ANY,ANY-method Man page
[,GenoGAMDataSet,GRanges,ANY,ANY-method Man page
[,GenoGAMDataSetList,GRanges,ANY,ANY-method Man page
[,GenoGAMList,GRanges,ANY,ANY-method Man page
asCoordinates Man page
assay,GenoGAM,missing-method Man page
assay,GenoGAMDataSetList,ANY-method Man page
assay,GenoGAMList,missing-method Man page
assays,GenoGAMDataSetList-method Man page
assays,GenoGAMList-method Man page
callPeaks Man page Source code
colData Man page
colData,GenoGAM-method Man page
colData,GenoGAMDataSetList-method Man page
colData,GenoGAMList-method Man page
colnames Man page
colnames,GenoGAM-method Man page
colnames,GenoGAMDataSetList-method Man page
colnames,GenoGAMList-method Man page
computeRegionSignificance Man page Source code
computeSignificance Man page Source code
computeSizeFactors Man page Source code
compute_pen_hessian Source code
compute_stdError Source code
dataRange Man page
dataRange,GenoGAMDataSet-method Man page
dataRange,GenoGAMDataSetList-method Man page
design,GenoGAM-method Man page
design,GenoGAMDataSet-method Man page
design,GenoGAMDataSetList-method Man page
design,GenoGAMList-method Man page
design<-,GenoGAMDataSet,ANY-method Man page
design<-,GenoGAMDataSetList,ANY-method Man page
dim,GenoGAMDataSetList-method Man page
dim,GenoGAMList-method Man page
dimnames Man page
dimnames,GenoGAM-method Man page
dimnames,GenoGAMList-method Man page
end,Coordinates-method Man page
end<-,Coordinates-method Man page
fits Man page
fits,GenoGAM-method Man page
fits,GenoGAMList-method Man page
genogam Man page Source code
getChromosomes Man page
getChromosomes,GenoGAMDataSet-method Man page
getChromosomes,GenoGAMDataSetList-method Man page
getChunkSize Man page
getChunkSize,GenoGAMDataSet-method Man page
getChunkSize,GenoGAMDataSetList-method Man page
getChunkSize<- Man page
getChunkSize<-,GenoGAMDataSet,numeric-method Man page
getChunkSize<-,GenoGAMDataSetList,numeric-method Man page
getCoefs Man page
getCoefs,GenoGAM-method Man page
getCoefs,GenoGAMList-method Man page
getCountMatrix,GenoGAMDataSet-method Man page
getCountMatrix,GenoGAMDataSetList-method Man page
getFamily Man page
getFamily,GenoGAM-method Man page
getFamily,GenoGAMList-method Man page
getIndex Man page
getIndex,GenoGAMDataSet-method Man page
getIndex,GenoGAMDataSetList-method Man page
getKnots Man page
getKnots,GenoGAM-method Man page
getKnots,GenoGAMList-method Man page
getOverhangSize Man page
getOverhangSize,GenoGAMDataSet-method Man page
getOverhangSize,GenoGAMDataSetList-method Man page
getOverhangSize<- Man page
getOverhangSize<-,GenoGAMDataSet,numeric-method Man page
getOverhangSize<-,GenoGAMDataSetList,numeric-method Man page
getParams Man page
getParams,GenoGAM-method Man page
getParams,GenoGAMList-method Man page
getSettings Man page
getSettings,GenoGAM-method Man page
getSettings,GenoGAMList-method Man page
getTileNumber Man page
getTileNumber,GenoGAMDataSet-method Man page
getTileNumber,GenoGAMDataSetList-method Man page
getTileNumber<- Man page
getTileNumber<-,GenoGAMDataSet,numeric-method Man page
getTileNumber<-,GenoGAMDataSetList,numeric-method Man page
getTileSize Man page
getTileSize,GenoGAMDataSet-method Man page
getTileSize,GenoGAMDataSetList-method Man page
getTileSize<- Man page
getTileSize<-,GenoGAMDataSet,numeric-method Man page
getTileSize<-,GenoGAMDataSetList,numeric-method Man page
gr_ll_pen_nb Source code
is.HDF5,GenoGAM-method Man page
is.HDF5,GenoGAMDataSet-method Man page
is.HDF5,GenoGAMDataSetList-method Man page
is.HDF5,GenoGAMList-method Man page
length,Coordinates-method Man page
length,GenoGAMDataSetList-method Man page
length,GenoGAMList-method Man page
ll_pen_nb Source code
ll_pen_qbd Source code
mad,GenoGAMDataSet-method Man page
mad,GenoGAMDataSetList-method Man page
makeTestGenoGAM Man page Source code
makeTestGenoGAMDataSet Man page Source code
makeTestGenoGAMDataSetList Man page Source code
makeTestGenoGAMList Man page Source code
mean,GenoGAMDataSet-method Man page
mean,GenoGAMDataSetList-method Man page
median,GenoGAMDataSet-method Man page
median,GenoGAMDataSetList-method Man page
ncol,Coordinates-method Man page
negbin_hessian Source code
nrow,Coordinates-method Man page
plotGenoGAM Man page Source code
plot_base Source code
pvalue,GenoGAM-method Man page
pvalue,GenoGAMList-method Man page
readData Man page Source code
rowRanges,GenoGAMDataSetList-method Man page
rowRanges,GenoGAMList-method Man page
sd,GenoGAMDataSet-method Man page
sd,GenoGAMDataSetList-method Man page
se Man page
se,GenoGAM-method Man page
se,GenoGAMList-method Man page
seqlengths,GenoGAMDataSetList-method Man page
seqlengths,GenoGAMList-method Man page
seqlevels,GenoGAMDataSetList-method Man page
seqlevels,GenoGAMList-method Man page
seqlevelsInUse,GenoGAMDataSetList-method Man page
seqlevelsInUse,GenoGAMList-method Man page
setupGenoGAM Source code
sizeFactors,GenoGAM-method Man page
sizeFactors,GenoGAMDataSet-method Man page
sizeFactors,GenoGAMDataSetList-method Man page
sizeFactors,GenoGAMList-method Man page
sizeFactors<-,GenoGAMDataSet,ANY-method Man page
sizeFactors<-,GenoGAMDataSetList,ANY-method Man page
start,Coordinates-method Man page
start<-,Coordinates-method Man page
subset,GenoGAMDataSet-method Man page
subset,GenoGAMDataSetList-method Man page
subset,GenoGAMList-method Man page
subsetByOverlaps,GenoGAMDataSet,GRanges-method Man page
subsetByOverlaps,GenoGAMDataSetList,GRanges-method Man page
subsetByOverlaps,GenoGAMList,GRanges-method Man page
tileSettings Man page
tileSettings,GenoGAMDataSet-method Man page
tileSettings,GenoGAMDataSetList-method Man page
var,GenoGAMDataSet,ANY-method Man page
var,GenoGAMDataSetList,ANY-method Man page
width,Coordinates-method Man page
writeToBEDFile Man page Source code
writeToBroadPeaks Source code
writeToNarrowPeaks Source code
GenoGAM documentation built on Nov. 8, 2020, 7:45 p.m.

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