Man pages for CoGAPS
Coordinated Gene Activity in Pattern Sets

binaryA-methodsbinary heatmap for standardized feature matrix
buildReportInformation About Package Compilation
calcCoGAPSStat-methodscalculate statistic on sets of measurements (genes) or...
calcGeneGSStat-methodsprobability gene belongs in gene set
calcZ-methodscompute z-score matrix
callInternalCoGAPSmake correct call to internal CoGAPS dispatch function,...
checkDataMatrixcheck that provided data is valid
checkInputscheck that all inputs are valid
checkpointsEnabledCheck if package was built with checkpoints enabled
CoGAPSCoGAPS Matrix Factorization Algorithm
CoGAPS-packageCoGAPS: Coordinated Gene Activity in Pattern Sets
CogapsParamsCogapsParams constructor
compiledWithOpenMPSupportCheck if compiler supported OpenMP
computeGeneGSProb-methodscompute gene probability
convertDataToMatrixconvert any acceptable data input to a numeric matrix
corcutcluster patterns together
corrToMeanPatterncalculate correlation of each pattern in a cluster to the...
createCogapsResultconvert list output from c++ code to a CogapsResult object
createSetspartition genes/samples into subsets
distributedCogapsCoGAPS Distributed Matrix Factorization Algorithm
findConsensusMatrixfind the consensus pattern matrix across all subsets
gapsCatwrapper around cat
getAmplitudeMatrix-methodsreturn Amplitude matrix from CogapsResult object
getClusteredPatterns-methodsreturn clustered patterns from set of all patterns across all...
getCorrelationToMeanPattern-methodsreturn correlation between each pattern and the cluster mean
getDimNamesextracts gene/sample names from the data
getFeatureLoadings-methodsreturn featureLoadings matrix from CogapsResult object
getGeneNamesextract gene names from data
getMeanChiSq-methodsreturn chi-sq of final matrices
getOriginalParameters-methodsreturn original parameters used to generate this result
getParam-methodsget the value of a parameter
getPatternMatrix-methodsreturn pattern matrix from CogapsResult object
getRetinaSubsetget specified number of retina subsets
getSampleFactors-methodsreturn sampleFactors matrix from CogapsResult object
getSampleNamesextract sample names from data
getSubsets-methodsreturn the names of the genes (samples) in each subset
getUnmatchedPatterns-methodsreturn unmatched patterns from each subset
getValueOrRdsget input that might be an RDS file
getVersion-methodsreturn version number used to generate this result
GIST.data_frameGIST gene expression data from Ochs et al. (2009)
GIST.matrixGIST gene expression data from Ochs et al. (2009)
GIST.resultCoGAPS result from running on GIST dataset
GIST.uncertaintyGIST gene expression uncertainty matrix from Ochs et al....
initialize-CogapsParams-methodconstructor for CogapsParams
initialize-CogapsResult-methodConstructor for CogapsResult
isRdsFilechecks if file is rds format
ncolHelperget number of columns from supported file name or matrix
nrowHelperget number of rows from supported file name or matrix
parseExtraParamsparse parameters passed through the ... variable
patternMarkers-methodscompute pattern markers statistic
patternMatchMatch Patterns Across Multiple Runs
plotPatternMarkers-methodsheatmap of original data clustered by pattern markers...
plotResiduals-methodsplot of residuals
reconstructGene-methodsreconstruct gene
sampleUniformlysubset data by uniformly partioning rows (cols)
sampleWithAnnotationWeightssubset rows (cols) proportional to the user provided weights
sampleWithExplictSetsuse user provided subsets
scCoGAPSSingle Cell CoGAPS
setAnnotationWeights-methodsset the annotation labels and weights for subsetting the data
setDistributedParams-methodsset the value of parameters for distributed CoGAPS
setFixedPatterns-methodsset the fixed patterns for either the A or the P matrix
setParam-methodsset the value of a parameter
startupMessagewrite start up message
stitchTogetherconcatenate final results across subsets
supportedchecks if file is supported
CoGAPS documentation built on Nov. 8, 2020, 5:02 p.m.