# Coordinated Gene Activity in Pattern Sets

## Documentation for package ‘CoGAPS’ version 3.0.2

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

## 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.