Man pages for CoGAPS/CoGAPS
Coordinated Gene Activity in Pattern Sets
| binaryA-methods | binary heatmap for standardized feature matrix |
| buildReport | Information About Package Compilation |
| calcCoGAPSStat-methods | calculate statistic on sets of measurements (genes) or... |
| calcGeneGSStat-methods | probability gene belongs in gene set |
| calcZ-methods | compute z-score matrix |
| callInternalCoGAPS | make correct call to internal CoGAPS dispatch function,... |
| checkDataMatrix | check that provided data is valid |
| checkInputs | check that all inputs are valid |
| checkpointsEnabled | Check if package was built with checkpoints enabled |
| CoGAPS | CoGAPS Matrix Factorization Algorithm |
| CoGAPS-package | CoGAPS: Coordinated Gene Activity in Pattern Sets |
| CogapsParams | CogapsParams constructor |
| CogapsParams-class | CogapsParams |
| CogapsResult-class | CogapsResult |
| compiledWithOpenMPSupport | Check if compiler supported OpenMP |
| computeGeneGSProb-methods | compute gene probability |
| convertDataToMatrix | convert any acceptable data input to a numeric matrix |
| corcut | cluster patterns together |
| corrToMeanPattern | calculate correlation of each pattern in a cluster to the... |
| createCogapsResult | convert list output from c++ code to a CogapsResult object |
| createSets | partition genes/samples into subsets |
| distributedCogaps | CoGAPS Distributed Matrix Factorization Algorithm |
| findConsensusMatrix | find the consensus pattern matrix across all subsets |
| fromCSV-methods | read CoGAPS Result object from a directory with a set of csvs... |
| gapsCat | wrapper around cat |
| getAmplitudeMatrix-methods | return Amplitude matrix from CogapsResult object |
| getClusteredPatterns-methods | return clustered patterns from set of all patterns across all... |
| getCorrelationToMeanPattern-methods | return correlation between each pattern and the cluster mean |
| getDimNames | extracts gene/sample names from the data |
| getFeatureLoadings-methods | return featureLoadings matrix from CogapsResult object |
| getGeneNames | extract gene names from data |
| getMeanChiSq-methods | return chi-sq of final matrices |
| getOriginalParameters-methods | return original parameters used to generate this result |
| getParam-methods | get the value of a parameter |
| getPatternGeneSet-methods | generate statistics associating patterns with gene sets |
| getPatternMatrix-methods | return pattern matrix from CogapsResult object |
| getRetinaSubset | get specified number of retina subsets |
| getSampleFactors-methods | return sampleFactors matrix from CogapsResult object |
| getSampleNames | extract sample names from data |
| getSubsets-methods | return the names of the genes (samples) in each subset |
| getUnmatchedPatterns-methods | return unmatched patterns from each subset |
| getValueOrRds | get input that might be an RDS file |
| getVersion-methods | 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.... |
| GWCoGAPS | Genome Wide CoGAPS |
| initialize-CogapsParams-method | constructor for CogapsParams |
| initialize-CogapsResult-method | Constructor for CogapsResult |
| isRdsFile | checks if file is rds format |
| MANOVA-methods | MANOVA statistical test for patterns between sample groups |
| modsimdata | Toy example to run CoGAPS on. |
| modsimresult | Result of applying CoGAPS on the Toy example. |
| ncolHelper | get number of columns from supported file name or matrix |
| nrowHelper | get number of rows from supported file name or matrix |
| parseExtraParams | parse parameters passed through the ... variable |
| patternMarkers-methods | compute pattern markers statistic |
| patternMatch | Match Patterns Across Multiple Runs |
| plotPatternGeneSet-methods | generate a barchart of most significant hallmark sets for a... |
| plotPatternMarkers-methods | heatmap of original data clustered by pattern markers... |
| plotResiduals-methods | plot of residuals |
| reconstructGene-methods | reconstruct gene |
| sampleUniformly | subset data by uniformly partioning rows (cols) |
| sampleWithAnnotationWeights | subset rows (cols) proportional to the user provided weights |
| sampleWithExplictSets | use user provided subsets |
| scCoGAPS | Single Cell CoGAPS |
| setAnnotationWeights-methods | set the annotation labels and weights for subsetting the data |
| setDistributedParams-methods | set the value of parameters for distributed CoGAPS |
| setFixedPatterns-methods | set the fixed patterns for either the A or the P matrix |
| setParam-methods | set the value of a parameter |
| startupMessage | write start up message |
| stitchTogether | concatenate final results across subsets |
| supported | checks if file is supported |
| toCSV-methods | save CoGAPS Result object as a set of csvs to directory see... |
