binaryA                 binary heatmap for standardized feature matrix
buildReport             Information About Package Compilation
calcCoGAPSStat          calculate statistic on sets of measurements
                        (genes) or samples
calcGeneGSStat          probability gene belongs in gene set
calcZ                   compute z-score matrix
checkpointsEnabled      Check if package was built with checkpoints
                        enabled
CoGAPS                  CoGAPS Matrix Factorization Algorithm
CoGAPS-package          CoGAPS: Coordinated Gene Activity in Pattern
                        Sets
CogapsParams            CogapsParams constructor
CogapsParams-class      CogapsParams
CogapsResult-class      CogapsResult
compiledWithOpenMPSupport
                        Check if compiler supported OpenMP
computeGeneGSProb       compute gene probability
findConsensusMatrix     find the consensus pattern matrix across all
                        subsets
fromCSV                 read CoGAPS Result object from a directory with
                        a set of csvs see toCSV
getAmplitudeMatrix      return Amplitude matrix from CogapsResult
                        object
getClusteredPatterns    return clustered patterns from set of all
                        patterns across all subsets
getCorrelationToMeanPattern
                        return correlation between each pattern and the
                        cluster mean
getFeatureLoadings      return featureLoadings matrix from CogapsResult
                        object
getMeanChiSq            return chi-sq of final matrices
getOriginalParameters   return original parameters used to generate
                        this result
getParam                get the value of a parameter
getPatternGeneSet       generate statistics associating patterns with
                        gene sets
getPatternMatrix        return pattern matrix from CogapsResult object
getRetinaSubset         get specified number of retina subsets
getSampleFactors        return sampleFactors matrix from CogapsResult
                        object
getSubsets              return the names of the genes (samples) in each
                        subset
getUnmatchedPatterns    return unmatched patterns from each subset
getVersion              return version number used to generate this
                        result
GIST.data_frame         GIST gene expression data from Ochs et al.
                        (2009)
GIST.matrix             GIST gene expression data from Ochs et al.
                        (2009)
GIST.result             CoGAPS result from running on GIST dataset
GIST.uncertainty        GIST gene expression uncertainty matrix from
                        Ochs et al. (2009)
GWCoGAPS                Genome Wide CoGAPS
initialize,CogapsParams-method
                        constructor for CogapsParams
initialize,CogapsResult-method
                        Constructor for CogapsResult
MANOVA                  MANOVA statistical test for patterns between
                        sample groups
modsimdata              Toy example to run CoGAPS on.
modsimresult            Result of applying CoGAPS on the Toy example.
patternMarkers          compute pattern markers statistic
plotPatternGeneSet      generate a barchart of most significant
                        hallmark sets for a pattern
plotPatternMarkers      heatmap of original data clustered by pattern
                        markers statistic
plotResiduals           plot of residuals
reconstructGene         reconstruct gene
scCoGAPS                Single Cell CoGAPS
setAnnotationWeights    set the annotation labels and weights for
                        subsetting the data
setDistributedParams    set the value of parameters for distributed
                        CoGAPS
setFixedPatterns        set the fixed patterns for either the A or the
                        P matrix
setParam                set the value of a parameter
toCSV                   save CoGAPS Result object as a set of csvs to
                        directory see fromCSV
