# Coordinated Gene Activity in Pattern Sets

## Documentation for package ‘CoGAPS’ version 3.31.0

- 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 feature matrix
binaryA-method | binary heatmap for standardized feature matrix
buildReport | Information About Package Compilation
calcCoGAPSStat | calculate statistic on sets of measurements (genes) or samples
calcCoGAPSStat-method | calculate statistic on sets of measurements (genes) or samples
calcGeneGSStat | probability gene belongs in gene set
calcGeneGSStat-method | probability gene belongs in gene set
calcZ | compute z-score matrix
calcZ-method | compute z-score matrix
checkpointsEnabled | Check if package was built with checkpoints enabled
CoGAPS | CoGAPS Matrix Factorization Algorithm
CogapsParams | CogapsParams constructor
CogapsParams-class | CogapsParams
CogapsResult-class | CogapsResult
compiledWithOpenMPSupport | Check if compiler supported OpenMP
computeGeneGSProb | compute gene probability
computeGeneGSProb-method | compute gene probability
findConsensusMatrix | find the consensus pattern matrix across all subsets
fromCSV | read CoGAPS Result object from a directory with a set of csvs see toCSV
fromCSV-method | read CoGAPS Result object from a directory with a set of csvs see toCSV
getAmplitudeMatrix | return Amplitude matrix from CogapsResult object
getAmplitudeMatrix-method | return Amplitude matrix from CogapsResult object
getClusteredPatterns | return clustered patterns from set of all patterns across all subsets
getClusteredPatterns-method | return clustered patterns from set of all patterns across all subsets
getCorrelationToMeanPattern | return correlation between each pattern and the cluster mean
getCorrelationToMeanPattern-method | return correlation between each pattern and the cluster mean
getFeatureLoadings | return featureLoadings matrix from CogapsResult object
getFeatureLoadings-method | return featureLoadings matrix from CogapsResult object
getMeanChiSq | return chi-sq of final matrices
getMeanChiSq-method | return chi-sq of final matrices
getOriginalParameters | return original parameters used to generate this result
getOriginalParameters-method | return original parameters used to generate this result
getParam | get the value of a parameter
getParam-method | get the value of a parameter
getPatternGeneSet | generate statistics associating patterns with gene sets
getPatternGeneSet-method | generate statistics associating patterns with gene sets
getPatternMatrix | return pattern matrix from CogapsResult object
getPatternMatrix-method | return pattern matrix from CogapsResult object
getRetinaSubset | get specified number of retina subsets
getSampleFactors | return sampleFactors matrix from CogapsResult object
getSampleFactors-method | return sampleFactors matrix from CogapsResult object
getSubsets | return the names of the genes (samples) in each subset
getSubsets-method | return the names of the genes (samples) in each subset
getUnmatchedPatterns | return unmatched patterns from each subset
getUnmatchedPatterns-method | return unmatched patterns from each subset
getVersion | return version number used to generate this result
getVersion-method | return version number used to generate this result
GIST.data_frame | GIST gene expression data from Ochs et al. (2009)
GIST.matrix | GIST gene expression data from Ochs et al. (2009)
GIST.result | CoGAPS result from running on GIST dataset
GIST.uncertainty | GIST gene expression uncertainty matrix from Ochs et al. (2009)
GWCoGAPS | Genome Wide CoGAPS
initialize-method | constructor for CogapsParams
initialize-method | Constructor for CogapsResult
MANOVA | MANOVA statistical test for patterns between sample groups
MANOVA-method | MANOVA statistical test for patterns between sample groups
modsimdata | Toy example to run CoGAPS on.
modsimresult | Result of applying CoGAPS on the Toy example.
patternMarkers | compute pattern markers statistic
patternMarkers-method | compute pattern markers statistic
plotPatternGeneSet | generate a barchart of most significant hallmark sets for a pattern
plotPatternGeneSet-method | generate a barchart of most significant hallmark sets for a pattern
plotPatternMarkers | heatmap of original data clustered by pattern markers statistic
plotResiduals | plot of residuals
plotResiduals-method | plot of residuals
reconstructGene | reconstruct gene
reconstructGene-method | reconstruct gene
scCoGAPS | Single Cell CoGAPS
setAnnotationWeights | set the annotation labels and weights for subsetting the data
setAnnotationWeights-method | set the annotation labels and weights for subsetting the data
setDistributedParams | set the value of parameters for distributed CoGAPS
setDistributedParams-method | set the value of parameters for distributed CoGAPS
setFixedPatterns | set the fixed patterns for either the A or the P matrix
setFixedPatterns-method | set the fixed patterns for either the A or the P matrix
setParam | set the value of a parameter
setParam-method | set the value of a parameter
toCSV | save CoGAPS Result object as a set of csvs to directory see fromCSV
toCSV-method | save CoGAPS Result object as a set of csvs to directory see fromCSV