A Package for De Novo CNV Detection in Case-Parent Trios

acf2 | Function for computing autocorrelations |

calculateMindist | Deprecated function to calculate the minimum distance |

coercion-methods | Coerces a TrioSetList to a TrioSet |

Defunct | Defunct functions/classes/methods in the MinimumDistance... |

denovo | Filter the genomic intervals for denovo copy number states |

Deprecated | Deprecated functions and methods |

DNAcopyParam | Constructor for DNAcopyParam class |

exampleTrioSetList | An example 'TrioSetList' object |

filterExperiment | Methods for filtering MinDistExperiment objects |

FilterParamMD | Parameters for filtering results from the segmentation and... |

FilterParamMD-class | A class for filtering genomic intervals called by... |

mad2 | Deprecated wrapper for computing the median absolute... |

MAP | Computes the maximum a posteriori trio copy number state for... |

MAP2 | Computes maximum a posteriori estimate for the trio copy... |

md_exp | An example 'MinDistExperiment' |

md_gr | An example 'MinDistGRanges' object |

mdLegend | Text summary of information encapculated in a MDRanges object... |

MDRanges-class | A 'GRanges'-derived class |

mindist | Getter and setter for the minimum distance statistic |

MinDistExperiment | Constructor for 'MinDistExperiment' class |

MinDistExperiment-class | Class and methods for MinDistExperiment |

MinDistGRanges | Constructor for 'MinDistGRanges' class |

MinDistGRanges-class | A container for storing segmentation data for members in a... |

MinDistParam | Constructor for 'MinDistParam' class |

MinDistParam-class | Class and methods for parameters of minimum distance... |

MinDistPosterior-class | Container for the segmentation results from a... |

MinimumDistance | De novo copy number alterations in parent-offspring trios |

nMAD | Setter and getter for number of median absolute deviations... |

ParentOffspring-class | Object containing the sample identifiers for members in a... |

ParentOffspringList-class | A list of 'ParentOffspring' objects |

Pedigree | Deprecated function for constructing an instance of class... |

Pedigree-class | Deprecated class for storing pedigree data |

pedigreeGrid | Plot the log R ratios and BAFs on a grid given by precomputed... |

pedigreeName | Accessor for pedigree name |

pedigreeViewports | Default viewports for plotting log R ratios, BAFs, chromosome... |

PennParam | Constructor for class 'PennParam' |

plotDenovo | Plot marker-level summaries for a genomic interval of... |

range-ILimit-method | compute the range of an ILimit instance |

segment2 | A wrapper for DNAcopy's segment function |

TrioSet | Deprecated constructor for 'TrioSet' class |

TrioSet-class | Deprecated class for storing low-level genomic data for trios |

TrioSetList | Constructor for 'TrioSetList' class |

TrioSetList-class | Deprecated class for storing low-level genomic data for trios |

TrioSetListLD | Deprecated TrioSetList constructor for large data |

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