Identify Genes Overexpressed in Subsets of Tumors from Tumor-Normal mRNA Expression Data

colTrans | A pseudo transparency to a color |

createCNVmatrixForUCisoform | Gathering CNV Information for UCSC Isoform(s) from Multiple... |

distributionPlot | Generate a plot of all distributions indicated |

donut | Plot a donut |

entropy | Compute entropy (base e) from a vector of probabilities |

genClinMatrix | Generate a Clinical Matrix from TCGA data |

getMixModelParams | Generate the parameters for two 2-component mixture models... |

mergeLevels | Merge levels of a factor |

mixModelParams | Generate the parameters for two 2-component mixture models... |

na.mean | Replace NAs with mean |

na.zero | Replace NAs with zeros |

numericalize | Function to convert factors to numeric |

oncoMixBimodal | Creating an schematic of a 2-component mixture model |

oncoMixIdeal | Creating an ideal oncoMix gene |

oncoMixTraditionalDE | Creating an schematic of a traditional differential... |

rotatedLabel | Plot a rotated axis label |

scatterMix | Generate a scatter plot with the output from... |

scatterMixPlot | Generate a scatter plot with the output from... |

selectivityIndex | Calculate the selectivity Index from getMixModelParams |

sig2star | Function to transform P-values into symbols of significance... |

stars | Stars plot |

violinJitter | Jitter by violins |

violinJitterPlot | Violins plot with jittered data points |

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