Collection of functions for daily tasks

agg | Aggregate epxression |

assignCl | Assign class for test data based based on correlation |

boxGraph | Plot some position preserving boxplots |

cant | Cantor |

createPatChar | Create patient characteristics table |

detClusters | Determine number of clusters |

determineClass | Tried to determine the class of data.frame columns |

drawSegments | Draw segments for boxplots |

drawSpiralPlot | Draw spiral plot |

encCant | Cantor Encode |

exportSUMO | Export SUMO matrix |

expSUMO | Export to SUMO |

feAnalyze | Analyze fixed Effects |

filter | Keep only most variant |

findAssoc | Find associations |

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 |

fixedEffAnalysis | Model based analysis with fixed effects |

impSUMO | Import from SUMO |

initialize-matrixSUMO-method | Construcotr matrixSUMO |

localCor | Calculate genimc local correlation |

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 |

permTTest | Permutation t-test |

plotForest | Calculated univariate analysis and creates a forest plot |

plotForestMV | Calculates multivariate analysis and creates a forest plot |

plotForestOR | Calculated univariate analysis and creates a forest plot |

plotForestSplit | Create forest plot |

plotKM | Plots a Kaplan Meier survival curve with number at risk table |

plotSingle | Plot single gene |

preparePdf | Create tex/pdf files |

printHCLCand | Print Kaplan Meier plots |

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 |

simLoc450k | Calculate localtion sensitive similarity, 450k |

transf | Transform expression data |

tTest | Row-wise t-Test |

wy | Westfall Young p-value correction |

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