Man pages for mknoll/dataAnalysisMisc
Collection of functions for daily tasks
| agg | Aggregate epxression |
| assignCl | Assign class for test data based based on correlation |
| barnP | Barnards test (parallel) |
| boxGraph | Plot some position preserving boxplots |
| cant | Cantor |
| cnvAug | Augments segment breaks (plottign of steps) |
| cnvEval | Evaluate overlaps between segments |
| cnvOverlap | Prepare data for CNV overlap comparison |
| cnvSegGene | Get genes in overlapping segments |
| createGrids | Create grid |
| createPatChar | Create patient characteristics table |
| cv | Crossvalidate linear model |
| detClusters | Determine number of clusters |
| determineClass | Tried to determine the class of data.frame columns |
| dissimM | Compute dissim matrix |
| dotPlot | Dot plot for cor + p-val |
| drawSegments | Draw segments for boxplots |
| drawSpiralPlot | Draw spiral plot |
| encCant | Cantor Encode |
| equivFract | Test for euqivalence of proportions |
| exportSUMO | Export SUMO matrix |
| expSUMO | Export to SUMO |
| feAnalyze | Analyze fixed Effects |
| filter | Keep only most variant |
| findAssoc | Find associations |
| findCNVClusters | Find Clusters in CNV data |
| findHCLSurv | Find hierarchical cluster-based groups for survival... |
| findOptCutoff | Find two differening groups in survival data |
| findOptCutoffClass | Detect the best cutoff to match a categorical classification |
| findOptCutoff_Model | Find two differening groups in survival data |
| fitM | Fit model |
| fitModel-class | A S4 class representing an analysis |
| fixedEffAnalysis | Model based analysis with fixed effects |
| getMeans | Get Means |
| getMeansMT | Get Means (MT) |
| getMF | Most frequent number per col of integer matrix |
| getQuantiles | Get Quantiles from grid |
| impSUMO | Import from SUMO |
| initialize-fitModel-method | Constructor fitModel |
| initialize-matrixSUMO-method | Construcotr matrixSUMO |
| int | Intervals for parametric dist |
| localCor | Calculate genimc local correlation |
| matchPattern | Test occurence of substring |
| matchSub | Match and subst seq |
| matchSubRev | Match and subst seq rev |
| matrixSUMO-class | An S4 class representing a SUMO matrix experiment |
| minimizeMissclassificationHCL | Minimize missclassification by step-wise increase of... |
| mlt | Melt and merge data w/ pheno info |
| mutMatrix | Create mut matrix |
| permTTest | Permutation t-test |
| plotCNVChr | Plot different groups of samples based on CNV alterations |
| plotDiff | Plot pairwise comparisons of grids |
| plotDiff2 | Plot pairwise comparisons of grids |
| plotForest | Calculated univariate analysis and creates a forest plot |
| plotForestMV | Calculates multivariate analysis and creates a forest plot |
| plotForestParam | Calculated univariate analysis and creates a forest plot |
| plotForestParamMV | Calculates multivariate analysis and creates a forest plot |
| plotForestSplit | Create forest plot |
| plotForestSubgroup | Calculated univariate analysis and creates a forest plot |
| plotForestSubgroupParam | Calculated univariate analysis and creates a forest plot |
| plotKM | Plots a Kaplan Meier survival curve with number at risk table |
| plotModel | Plot pred / trained |
| plotSingle | Plot single gene |
| preparePdf | Create tex/pdf files |
| printHCLCand | Print Kaplan Meier plots |
| quantifyDiff | Quantify differences from pairwise comparisons |
| randEffAnalysis | Model based analysis with random effects |
| renameVars | Rename variables in a data frame using a mapping file |
| rocDetail | Create ROC curve |
| sampleAdj | Sample clusters from adjacence matrix |
| segMerge | Merge segments |
| simLoc450k | Calculate localtion sensitive similarity, 450k |
| testSign | Test significance |
| transf | Transform expression data |
| tTest | Row-wise t-Test |
| wy | Westfall Young p-value correction |
