Man pages for CoGAPS/CoGAPS
Coordinated Gene Activity in Pattern Sets

binaryA'binaryA' creates a binarized heatmap of the A matrix in...
calcCoGAPSStat'calcCoGAPSStat' calculates the gene set statistics for each...
calcGeneGSStat'calcGeneGSStat' calculates the probability that a gene...
calcZ'calcZ' calculates the Z-score for each element based on...
CoGAPS'CoGAPS' calls the C++ MCMC code through gapsRun and performs...
CoGAPS-packageCoGAPS: Coordinated Gene Activity in Pattern Sets
computeGeneGSProbCoGAPS gene membership statistic
createGWCoGAPSSetscreateGWCoGAPSSets
gapsMapRun'gapsMapRun' calls the C++ MCMC code and performs Bayesian...
gapsMapTestRun'gapsMapTestRun' calls the C++ MCMC code and performs...
gapsRun'gapsRun' calls the C++ MCMC code and performs Bayesian...
gapsTestRun'gapsTestRun' calls the C++ MCMC code and performs Bayesian...
generateSeedsgenerateSeeds
GIST.DSample GIST gene expression data from Ochs et al. (2009).
GIST.SSample GIST gene expression data from Ochs et al. (2009).
GSetsSimulated dataset to quantify gene set membership.
GWCoGAPSGWCoGAPS
patternMarkerspatternMarkers
patternMatch4ParallelpatternMatch4Parallel
patternMatcherPatternMatcher Shiny Ap
plotAtoms'plotAtoms' a simple plot of the number of atoms from one of...
plotDiag'plotDiag' plots a series of diagnostic plots
plotGAPS'plotGAPS' plots the output A and P matrices as a heatmap and...
plotP'plotP' plots the P matrix in a line plot with error bars
plotPatternMarkersplotPatternMarkers
plotSmoothPatterns'plotSmoothPatterns' plots the output A and P matrices as a...
postFixed4ParallelpostFixed4Parallel
reconstructGenereconstruct Gene
reorderByPatternMatch'reorderByPatternMatch' plots the output A and P matrices as...
reOrderBySetreOrderBySet
residuals'residuals' calculate residuals and produce heatmap
SimpSim.ASimulated data
SimpSim.DSimulated data
SimpSim.PSimulated data
SimpSim.SSimulated data
tf2ugFCGene sets defined by transcription factors defined from...
CoGAPS/CoGAPS documentation built on Sept. 23, 2017, 6:45 a.m.