Coordinated Gene Activity in Pattern Sets

[Up] [Top]

Documentation for package ‘CoGAPS’ version 3.0.2

Help Pages

CoGAPS-package CoGAPS: Coordinated Gene Activity in Pattern Sets
binaryA Binary Heatmap for Standardized A Matrix
calcCoGAPSStat Calculate Gene Set Statistics
calcGeneGSStat Probability Gene Belongs in Gene Set
calcZ Compute Z-Score Matrix
cellMatchR cellMatchR
CoGAPS CoGAPS Matrix Factorization Algorithm
CoGapsFromCheckpoint Restart CoGAPS from Checkpoint File
computeGeneGSProb Compute Gene Probability
createGWCoGAPSSets Create Gene Sets for GWCoGAPS
createscCoGAPSSets Create Gene Sets for scCoGAPS
displayBuildReport Display Information About Package Compilation
gapsMapRun Backwards Compatibility with v2
gapsRun Backwards Compatibility with v2
generateSeeds Generate Seeds for Multiple Concurrent Runs
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
GWCoGapsFromCheckpoint Restart a GWCoGaps Run from Checkpoint
patternMarkers patternMarkers
patternMatch4Parallel patternMatch4Parallel
patternMatcher PatternMatcher Shiny Ap
plotAtoms Plot Number of Atoms
plotDiag Diagnostic Plots
plotGAPS Plot Decomposed A and P Matrices
plotP Plot the P Matrix
plotPatternMarkers plotPatternMarkers
plotSmoothPatterns Plot Smooth Patterns
postFixed4Parallel Post Processing of Parallel Output
postFixed4SC Post Processing of Parallel Output
reconstructGene Reconstruct Gene
reorderByPatternMatch Reorder By Pattern Match
reOrderBySet reOrderBySet
residuals Plot of Residuals
scCoGAPS scCoGAPS
scCoGapsFromCheckpoint Restart a scCoGAPS run from a Checkpoint
SimpSim.A Simulated data
SimpSim.D Simulated data
SimpSim.P Simulated data
SimpSim.result Simulated Data Results
SimpSim.S Simulated data
tf2ugFC Gene sets defined by transcription factors defined from TRANSFAC.