Coordinated Gene Activity in Pattern Sets
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Documentation for package ‘CoGAPS’ version 3.25.1
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| 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 |