API for CoGAPS/CoGAPS
Coordinated Gene Activity in Pattern Sets

Global functions
CoGAPS	Man page Source code
CoGAPS-package	Man page
CogapsParams	Man page Source code
CogapsParams-class	Man page
CogapsResult-class	Man page
GIST.data_frame	Man page
GIST.matrix	Man page
GIST.result	Man page
GIST.uncertainty	Man page
GWCoGAPS	Man page Source code
MANOVA	Man page
MANOVA,matrix,CogapsResult-method	Man page
binaryA	Man page
binaryA,CogapsResult-method	Man page
buildReport	Man page Source code
calcCoGAPSStat	Man page
calcCoGAPSStat,CogapsResult-method	Man page
calcGeneGSStat	Man page
calcGeneGSStat,CogapsResult-method	Man page
calcZ	Man page
calcZ,CogapsResult-method	Man page
callInternalCoGAPS	Man page Source code
checkDataMatrix	Man page Source code
checkInputs	Man page Source code
checkpointsEnabled	Man page Source code
checkpointsEnabled_cpp	Source code
cogaps_cpp	Source code
cogaps_from_file_cpp	Source code
compiledWithOpenMPSupport	Man page Source code
compiledWithOpenMPSupport_cpp	Source code
computeGeneGSProb	Man page
computeGeneGSProb,CogapsResult-method	Man page
convertDataToMatrix	Man page Source code
corcut	Man page Source code
corrToMeanPattern	Man page Source code
createCogapsResult	Man page Source code
createSets	Man page Source code
distributedCogaps	Man page Source code
findConsensusMatrix	Man page Source code
fromCSV	Man page
fromCSV,character-method	Man page
gapsCat	Man page Source code
getAmplitudeMatrix	Man page
getAmplitudeMatrix,CogapsResult-method	Man page
getBuildReport_cpp	Source code
getClusteredPatterns	Man page
getClusteredPatterns,CogapsResult-method	Man page
getCorrelationToMeanPattern	Man page
getCorrelationToMeanPattern,CogapsResult-method	Man page
getDimNames	Man page Source code
getFeatureLoadings	Man page
getFeatureLoadings,CogapsResult-method	Man page
getFileInfo_cpp	Source code
getGeneNames	Man page Source code
getMeanChiSq	Man page
getMeanChiSq,CogapsResult-method	Man page
getOriginalParameters	Man page
getOriginalParameters,CogapsResult-method	Man page
getParam	Man page
getParam,CogapsParams-method	Man page
getPatternGeneSet	Man page
getPatternGeneSet,CogapsResult,list,character-method	Man page
getPatternMatrix	Man page
getPatternMatrix,CogapsResult-method	Man page
getRetinaSubset	Man page Source code
getSampleFactors	Man page
getSampleFactors,CogapsResult-method	Man page
getSampleNames	Man page Source code
getSubsets	Man page
getSubsets,CogapsResult-method	Man page
getUnmatchedPatterns	Man page
getUnmatchedPatterns,CogapsResult-method	Man page
getValueOrRds	Man page Source code
getVersion	Man page
getVersion,CogapsResult-method	Man page
initialize,CogapsParams-method	Man page
initialize,CogapsResult-method	Man page
isRdsFile	Man page Source code
modsimdata	Man page
modsimresult	Man page
ncolHelper	Man page Source code
nrowHelper	Man page Source code
parseExtraParams	Man page Source code
patternMarkers	Man page
patternMarkers,CogapsResult-method	Man page
patternMatch	Man page Source code
plot.CogapsResult	Source code
plotPatternGeneSet	Man page
plotPatternGeneSet,list,numeric,numeric-method	Man page
plotPatternMarkers	Man page Source code
plotResiduals	Man page
plotResiduals,CogapsResult-method	Man page
reconstructGene	Man page
reconstructGene,CogapsResult-method	Man page
run_catch_unit_tests	Source code
sampleUniformly	Man page Source code
sampleWithAnnotationWeights	Man page Source code
sampleWithExplictSets	Man page Source code
scCoGAPS	Man page Source code
setAnnotationWeights	Man page
setAnnotationWeights,CogapsParams-method	Man page
setDistributedParams	Man page
setDistributedParams,CogapsParams-method	Man page
setFixedPatterns	Man page
setFixedPatterns,CogapsParams-method	Man page
setParam	Man page
setParam,CogapsParams-method	Man page
startupMessage	Man page Source code
stitchTogether	Man page Source code
supported	Man page Source code
toCSV	Man page
toCSV,CogapsResult,character-method	Man page
unitVector	Source code