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

Global functions
GenoGAM Man page Source code
GenoGAM-class Man page
GenoGAM-methods Man page
GenoGAMDataSet Man page Source code
GenoGAMDataSet-class Man page
GenoGAMDataSetFromConfig Source code
GenoGAMDataSetFromSE Source code
GenoGAMDataSetToDataFrame Man page Source code
GenoGAMSettings Man page Source code
GenoGAMSettings-class Man page
GenomicTiles Man page Source code
GenomicTiles-class Man page
GenomicTilesFromRawData Source code
GenomicTilesFromSE Source code
GenomicTilesToDataFrame Source code
IQR,GenomicTiles-method Man page
MetricsFun Source code
Summary,GenomicTiles-method Man page
[,GenoGAMDataSet,GRanges,ANY,ANY-method Man page
[,GenomicTiles,GRanges,ANY,ANY-method Man page
[[,GenomicTiles,numeric,ANY-method Man page
asDataFrame Man page
bspline Source code
callBroadPeaks Source code
callPeaks Man page Source code
centerFragments Source code
changeChromosomes Source code
changeChunkSize Source code
changeNumberOfTiles Source code
changeOverhangSize Source code
changeSettings Man page Source code
changeSettings,GenomicTiles,character-method Man page
changeTileSize Source code
checkChromosomes Source code
checkChunkSize Source code
checkGenomicTiles Source code
checkNumberOfTiles Source code
checkOverhangSize Source code
checkSettings Man page Source code
checkSettings,GenomicTiles-method Man page
checkTileSize Source code
chunkBAM Source code
colData,GenoGAM-method Man page
combineTrack Source code
commonSubstring Source code
computeBroadPeakSignificance Source code
computePeakSignificance Source code
computeRegionSignificance Man page Source code
computeSignificance Man page Source code
computeSizeFactors Man page Source code
computeSpline Source code
computeTileExtremes Source code
computeZscore Source code
compute_filter Source code
countFragments Source code
dataRange Man page
dataRange,GPos-method Man page
dataRange,GenomicTiles-method Man page
deseq Source code
design,GenoGAM-method Man page
design,GenoGAMDataSet-method Man page
design<-,GenoGAMDataSet,ANY-method Man page
doCrossValidation Source code
exactSubsetByOverlaps Source code
extractFullGenomicTiles Source code
extractGR Source code
extractGenomicTilesByBlocks Source code
extractGenomicTilesByIndex Source code
extractSplines Source code
filterData Man page Source code
find_root Source code
genogam Man page Source code
getChromosomes Man page
getChromosomes,GenomicTiles-method Man page
getChunkIndex Man page
getChunkIndex,GenomicTiles-method Man page
getChunkSize Man page
getChunkSize,GenomicTiles-method Man page
getCoordinates Man page
getCoordinates,GenomicTiles-method Man page
getExtremes Source code
getFits Man page
getFits,GenoGAM-method Man page
getFunctions Source code
getIndex Man page
getIndex,GenomicTiles-method Man page
getIndexCoordinates Man page
getIndexCoordinates,GenomicTiles-method Man page
getNumCols Source code
getOverhangSize Man page
getOverhangSize,GenomicTiles-method Man page
getPairedCenters Source code
getTile Man page Source code
getTile,GenomicTiles-method Man page
getTileNumber Man page
getTileNumber,GenomicTiles-method Man page
getTileSize Man page
getTileSize,GenomicTiles-method Man page
getVars Source code
guessFactorGroups Source code
leaveOutConsecutiveIntervals Source code
loglik Source code
mad,GenomicTiles-method Man page
makeCoordinates Source code
makeTestGenoGAM Man page Source code
makeTestGenoGAMDataSet Man page Source code
makeTestGenomicTiles Man page Source code
makeTiles Source code
mean,GenomicTiles-method Man page
median,GenomicTiles-method Man page
meltGTile Source code
mergeRanges Source code
nitCV Source code
normalize Source code
normalizeConfig Source code
parsePeaks Source code
plot.GenoGAM Man page Source code Source code
plotQC_GenoGAMDataSet Source code
plotQC_hist Source code
plot_base Source code
plot_ggplot2 Source code
processCountChunks Source code
pvals Source code
qcGenoGAMDataSet Source code
qualityCheck Man page Source code
readBAM Source code
readBED Source code
readData Source code
readRawData Source code
result Source code
rowRanges,GenoGAM-method Man page
sd,GenomicTiles-method Man page
showGenoGAM Source code
showGenoGAMSettings Source code
showGenomicTiles Source code
sizeFactors,GenoGAMDataSet-method Man page
sizeFactors<-,GenoGAMDataSet,ANY-method Man page
subset,GenoGAM-method Man page
subset,GenoGAMDataSet-method Man page
subset,GenomicTiles-method Man page
subsetByDoubleBrackets Source code
subsetByOverlaps Source code
subsetByOverlaps,GenoGAM,ANY-method Man page
subsetByOverlaps,GenoGAMDataSet,GRanges-method Man page
subsetByOverlaps,GenomicTiles,GRanges-method Man page
subsetByPosition Source code
subsetByRanges Source code
subsetGenomicTiles Source code
subsetGenomicTilesByOverlaps Source code
subsetIndeces Source code
tileSettings Man page
tileSettings,GenomicTiles-method Man page
unlistCoordinates Source code
untile Man page Source code
untile,GenomicTiles-method Man page
updateFormula Source code
validateBAMParamsType Source code
validateCVParamsType Source code
validateChromosomes Source code
validateCoordinatesType Source code
validateDesignType Source code Source code
validateExpDesignType Source code
validateFitParamsType Source code
validateFitsType Source code
validateGenoGAM Source code
validateGenoGAMDataSet Source code
validateGenoGAMSettings Source code
validateGenomicTiles Source code
validateIndexType Source code
validateOptimControlType Source code
validateOptimMethodType Source code
validatePositionsType Source code
validateProcessType Source code
validateSFType Source code
validateSettingsType Source code Source code
validateSmoothsType Source code
validateTileSettingsType Source code
validateVCovType Source code
var,GenomicTiles,ANY-method Man page
view Man page
view,GenoGAM-method Man page
view,GenomicTiles-method Man page
writeToBEDFile Man page Source code
writeToBroadPeaks Source code
writeToNarrowPeaks Source code
xsd Source code
Bioconductor-mirror/GenoGAM documentation built on Aug. 17, 2017, 3:44 p.m.