Man pages for wurst-theke/bratwurst
What the package does (short line)
| amariDistance | Compute amari type distance between two matrices |
| attributeComparisonSignatures | Preparation for relabelling and recolouring of a riverplot |
| build_granges_object | Build GRanges object from signature list |
| calculate_FI | Calculate F1 score |
| calculate_for_classifier_range | Title |
| computeAbsDelta | Compute delta between each column (signature) per row |
| computeAbsDelta4OptK | Computes absolut delta per feature for each signature given... |
| computeAmariDistances | Compute Amari Distances from [Wu et. al, PNAS 2016] |
| computeCoefVar | Compute the coeficient of variation per row in a matrix. |
| computeCopheneticCoeff | Compute Cophenetic correlation coefficient, TO BE IMPROVED |
| computeCpuFrobErrors | Title |
| computeEntropy | Compute 'shannon' entropy per region. High Entropy means... |
| computeEntropy4OptK | Computes entropy for each feature in optimal K W-matrix |
| computeFeatureStats | Compute Signature Combinations for W-matrix given optimal K |
| computeFisher4Regions | Title |
| computeFrobErrorStats | Compute basic statistics for Frobenius Errors |
| computeMeanDiff4SignatureCombs | Title |
| computeNES | Title |
| computePeakStats4Regions | Title |
| computePValue4FrobError | Compute p-value with t-test for running K |
| computeRecoveryAUC | Title |
| computeRegionFC | Title |
| computeRegionFC4GRlist | Title |
| computeRmdAUCs | Title |
| computeRunningPeakStats4Regions | Title |
| computeSignatureSpecificFeatures | Compute signature specific features |
| computeSilhoutteWidth | Compute Alexandrov Criterion -> Silhoutte Width |
| cosineDiss | Create distance matrix with cosine similarity |
| cosineDissMat | Create distance matrix with cosine similarity with matrix... |
| cosineDist | Cosine distance |
| cosineSim | Cosine similarity |
| extract_signature_specific_genes | Extract genes specfic for each signature |
| FeatureStats-nmfExperiment-method | Feature Statistics getter |
| filter_features | Filter features |
| filter_specific_features | Filter features which are specific for a single signature |
| FrobError-nmfExperiment-method | Frobenius Error getter |
| generate_classifier | Generate classifier |
| generateRiverplot | Generate a riverplot object that displays the similarities... |
| getColorAnno | Computes color annotation for colData from NMF-experiment... |
| getColorMap | Generate ColorMap for ComplexHeatmaps |
| getCpuHMatrixList | Getter function for H-Matrix list from NMF-CPU list |
| getCpuWMatrixList | Getter function for W-Matrix list from NMF-CPU list |
| getFrobError | Getter function for FrobError from NMF-GPU list |
| getHMatrixList | Getter function for H-Matrix list from NMF-GPU list |
| getIndex4SignatureCombs | Title |
| getSignatureCombCounts | Title |
| getSignatureNames | Compute unsupervised signature names from colData and... |
| getWMatrixList | Getter function for W-Matrix list from NMF-GPU list |
| HMatrixList-nmfExperiment-method | H-Matrix List getter |
| HMatrix-nmfExperiment-method | H-Matrix getter |
| igvCoord2Grange | Title |
| match_and_count | Match and count |
| merge.nmf | Merge two objects of type nmfExperiment |
| nmfExperiment-class | NMF Experiment Class |
| nmfExperimentFromFile | Reads Matrix & Annotation Files to SummarizedExperiment... |
| nmfExperimentFromMatrix | Convert Matrix to SummarizedExperiment Object |
| nnls_sol | Find non-negative exposures of one matrix in another matrix |
| normalizeH | Normalize the signatures matrix (H) |
| normalizeUpperQuartile | Title |
| normalizeW | Normalize the signatures matrix (W) |
| OptK-nmfExperiment-method | Optimal K |
| OptKStats-nmfExperiment-method | Optimal K Statistics getter |
| orderBinary | Function to order binary data matrix |
| performRowKmeans | Perform Kmeans on rows of a matrix to classify them into... |
| plotHeatmap4MatrixList | OLD VERSION MIGHT BE REMOVABLE Plot H or W-Matrix as heatmaps... |
| plotHMatrix | Plot H-Matrix as heatmap for a given factorization rank K |
| plotKStats | Universal ploting function for Optimal K Statistics |
| plotRankedFrobErrors | Ploting function for Rank vs. Frobenius Error |
| plotSignatureFeatures | Title |
| proposeOptK | Title |
| rankTransform | Title |
| regularizeH | Regularize the signatures matrix (H) |
| relabelRiverplot | Relabel and recolour a riverplot |
| reorderEdges | Order the riverplot edges to prevent crossings from a single... |
| runNmfCpu | Title |
| runNmfGpu | Title |
| runNmfGpuPyCuda | Title |
| science_theme | Science like figures - ggplot2 theme |
| setFeatureStats-nmfExperiment-method | Feature Statistics setter |
| setFrobError-nmfExperiment-method | Frobenius Error setter |
| setHMatrixList-nmfExperiment-method | H-Matrix List setter |
| setOptK-nmfExperiment-method | Optimal K setter |
| setOptKStats-nmfExperiment-method | Optimal K Statistics setter |
| setSignatureSpecificFeatures-nmfExperiment-method | Feature Statistics setter |
| setWMatrixList-nmfExperiment-method | W-Matrix setter |
| sigmoidTransform | Title |
| sigmoidTransform2 | Title |
| SignatureSpecificFeatures-nmfExperiment-method | Signature specfific features getter |
| translateBratwurstToYAPSA | Translate from Bratwurst to YAPSA |
| WMatrixList-nmfExperiment-method | W-Matrix list getter |
| WMatrix-nmfExperiment-method | W-Matrix getter |
| writeTmpMatrix | Title |
| yNodeCoords | Order the riverplot nodes to minimize crossings |
