# Coordinated Gene Activity in Pattern Sets

## Documentation for package ‘CoGAPS’ version 2.12.0

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

## Help Pages

CoGAPS-package | CoGAPS: Coordinated Gene Activity in 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 | '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
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
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
geneGSProb | CoGAPS gene membership statistic
generateSeeds | generateSeeds
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
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
reconstructGene | reconstruct Gene
reorderByPatternMatch | 'reorderByPatternMatch' plots the output A and P matrices as a heatmap and line plot respectively
reOrderBySet | reOrderBySet
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.