CoGAPS                  'CoGAPS' calls the C++ MCMC code through
                        gapsRun and performs Bayesian matrix
                        factorization returning the two matrices that
                        reconstruct the data matrix and then calls
                        calcCoGAPSStat to estimate gene set activity
                        with nPerm set to 500
CoGAPS-package          CoGAPS: Coordinated Gene Activity in Pattern
                        Sets
GIST.D                  Sample GIST gene expression data from Ochs et
                        al. (2009).
GIST.S                  Sample GIST gene expression data from Ochs et
                        al. (2009).
GSets                   Simulated dataset to quantify gene set
                        membership.
GWCoGAPS                GWCoGAPS
SimpSim.A               Simulated data
SimpSim.D               Simulated data
SimpSim.P               Simulated data
SimpSim.S               Simulated data
binaryA                 'binaryA' creates a binarized heatmap of the A
                        matrix in which the value is 1 if the value in
                        Amean is greater than threshold * Asd and 0
                        otherwise
calcCoGAPSStat          'calcCoGAPSStat' calculates the gene set
                        statistics for each column of A using a Z-score
                        from the elements of the A matrix, the input
                        gene set, and permutation tests
calcGeneGSStat          'calcGeneGSStat' calculates the probability
                        that a gene listed in a gene set behaves like
                        other genes in the set within the given data
                        set
calcZ                   'calcZ' calculates the Z-score for each element
                        based on input mean and standard deviation
                        matrices
computeGeneGSProb       CoGAPS gene membership statistic
createGWCoGAPSSets      createGWCoGAPSSets
gapsMapRun              'gapsMapRun' calls the C++ MCMC code and
                        performs Bayesian matrix factorization
                        returning the two matrices that reconstruct the
                        data matrix; as opposed to gapsRun, this method
                        takes an additional input specifying set
                        patterns in the P matrix
gapsMapTestRun          'gapsMapTestRun' calls the C++ MCMC code and
                        performs Bayesian matrix factorization
                        returning the two matrices that reconstruct the
                        data matrix; as opposed to gapsRun, this method
                        takes an additional input specifying set
                        patterns in the P matrix
gapsRun                 'gapsRun' calls the C++ MCMC code and performs
                        Bayesian matrix factorization returning the two
                        matrices that reconstruct the data matrix
gapsTestRun             'gapsTestRun' calls the C++ MCMC code and
                        performs Bayesian matrix factorization
                        returning the two matrices that reconstruct the
                        data matrix
generateSeeds           generateSeeds
patternMarkers          patternMarkers
patternMatch4Parallel   patternMatch4Parallel
patternMatcher          PatternMatcher Shiny Ap
plotAtoms               'plotAtoms' a simple plot of the number of
                        atoms from one of the vectors returned with
                        atom numbers
plotDiag                'plotDiag' plots a series of diagnostic plots
plotGAPS                'plotGAPS' plots the output A and P matrices as
                        a heatmap and line plot respectively
plotP                   'plotP' plots the P matrix in a line plot with
                        error bars
plotPatternMarkers      plotPatternMarkers
plotSmoothPatterns      'plotSmoothPatterns' plots the output A and P
                        matrices as a heatmap and line plot
                        respectively
postFixed4Parallel      postFixed4Parallel
reOrderBySet            reOrderBySet
reconstructGene         reconstruct Gene
reorderByPatternMatch   'reorderByPatternMatch' plots the output A and
                        P matrices as a heatmap and line plot
                        respectively
residuals               'residuals' calculate residuals and produce
                        heatmap
tf2ugFC                 Gene sets defined by transcription factors
                        defined from TRANSFAC.
