Statistics for Integrative Genomics Analyses in R

cghCall2cghSeg | Genomic ordering of cghSeg-objects. |

cghCall2maximumSubset | Maximum subsetting cghCall-objects. |

cghCall2order | Genomic ordering of cghCall-objects. |

cghCall2subset | Subsetting cghCall-objects. |

cghCall2weightedSubset | Weighted subsetting cghCall-objects. |

cghSeg2order | Genomic ordering of cghSeg-objects. |

cghSeg2subset | Subsetting cghSeg-objects. |

cghSeg2weightedSubset | Weighted subsetting cghSeg-objects. |

cisEffectPlot | DNA-mRNA plot |

cisEffectTable | Table of cis-effect test results |

cisEffectTest | Nonparametric testing for copy number induced differential... |

cisEffectTune | Pre-test and tuning. |

cisTest-class | Class "cisTest" for storing the results of the function... |

CNGEheatmaps | Parellel CN and GE heatmap plotting |

entropyTest | One-sided two-sample test for entropy comparison |

entTest-class | Class "entTest" for storing the results of the function... |

expandMatching2singleIDs | Expand matching to single entries |

ExpressionSet2order | Genomic ordering of ExpressionSet-objects. |

ExpressionSet2subset | Subsetting ExpressionSet-objects. |

ExpressionSet2weightedSubset | Weighted subsetting ExpressionSet-objects. |

getSegFeatures | Identical signature features selection from cghCall-object. |

hdEntropy | Entropy estimation. |

hdMI | Mutual information estimation. |

matchAnn2Ann | Genomic location matching of two sets of features |

matchCGHcall2ExpressionSet | Genomic location matching of CN and GE data |

merge2cghCalls | Merge two cghCall-objects into one cghCall-object |

merge2ExpressionSets | Merge two ExpressionSet-objects into one ExpressionSet-object |

miTest-class | Class "miTest" for storing the results of the function... |

mutInfTest | Test for mutual information |

nBreakpoints | Number of breakpoints |

pathway1sample | Penalized estimation of a pathyway's regulatory network from... |

pathway2sample | Penalized estimation of a pathyway's regulatory network from... |

pathwayFit-class | Class "pathwayFit" for storing the results of the function... |

pathwayPlot | Plot of the pathyway topology as reconstructed from from DNA... |

pollackCN16 | Breast cancer data (copy number) |

pollackGE16 | Breast cancer data (gene expression) |

profilesPlot | CN-GE profiles plot |

RCMestimation | Fitting of the random coefficients model. |

rcmFit-class | Class "rcmFit" for storing the results of the function... |

RCMrandom | Random data from the random coefficients model. |

RCMrandom-method | Methods for Function RCMrandom |

RCMtest | Hypothesis testing within the random coefficient model. |

rcmTest-class | Class "rcmTest" for storing the results of the function... |

sigaR-package | statistics for integrative genomics analyses in R |

splitMatchingAtBreakpoints | Split matching at breakpoints |

summary-method | Methods for Function summary |

uniqGenomicInfo | Unique genomic location information |

z.RCMloss-method | Internal function |

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