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 Analysis 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.
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          CoGAPS gene set statistic
computeGeneGSProb       CoGAPS gene membership statistic
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
gapsRun                 'gapsRun' calls the C++ MCMC code and performs
                        Bayesian matrix factorization returning the two
                        matrices that reconstruct the data matrix
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                Plotter for GAPS decomposition results
plotP                   'plotP' plots the P matrix in a line plot with
                        error bars
plotSmoothPatterns      Plot loess smoothed CoGAPS patterns
reorderByPatternMatch   Match two sets of patterns found with CoGAPS
residuals               'residuals' calculate residuals and produce
                        heatmap
tf2ugFC                 Gene sets defined by transcription factors
                        defined from TRANSFAC.
