# Coordinated Gene Activity in Pattern Sets

## Documentation for package ‘CoGAPS’ version 2.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

CoGAPS-package | CoGAPS: Coordinated Gene Analysis Pattern Sets
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
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
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
geneGSProb | CoGAPS gene membership statistic
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.
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
SimpSim.A | Simulated data
SimpSim.D | Simulated data
SimpSim.P | Simulated data
SimpSim.S | Simulated data
tf2ugFC | Gene sets defined by transcription factors defined from TRANSFAC.