A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

averageMatrixEdges | Average edges of a matrix to facilitate downsampling. |

calcCNVKernelProbDist | Calculate the probability distribution of CNV concordance... |

calcVecLMs | Create a linear regression matrix. |

CNVScopeserver | Server component of the CNVScope plotly shiny application. |

createChromosomalMatrixSet | Create chromosomal interaction matrices for CNVScope shiny... |

downsample_genomic_matrix | Rescale positive and negative data, preserving sign... |

extractNegLogPval | Find the negative log p-value of a pair of vectors. |

formSampleMatrixFromRawGDCData | Form sample matrix from GDC low-pass segmentation datafiles. |

freadGDCfile | Read GDC segmentation datafile for low-pass sequencing data. |

getAnnotationMatrix | Get the genes in the genomic ranges indicated by the row and... |

getAsymmetricBlockIndices | Get Block Indices from an asymmetric (or symmetric) matrix. |

getBlockAverageMatrixFromBreakpoints | Calculate block averages and areas in a matrix given... |

getGlobalRescalingStats | Calculate several base statistics for color rescaling. |

getInterchromosomalInteractivePlot | Create an HTML widget for use in shiny or webshot for a given... |

GRanges_to_underscored_pos | Convert GRanges object to underscord positions. |

importBreakpointBed | Import a breakpoint BED file. |

mathead | Gets a small piece of a matrix (top left corner) for viewing,... |

nbl_result_matrix_sign_small | Neuroblastoma sample CNV relationship matrix |

postProcessLinRegMatrix | Postprocess linear regression matrix. |

rebinGenomicInteractions | Assign GenomicInteractions to a predefined series of bins for... |

runCNVScopeLocal | Runs the CNVScope plotly shiny application. |

runCNVScopeShiny | Runs the CNVScope plotly shiny application. |

signedRescale | Rescale positive and negative data, preserving sign... |

underscored_pos_to_GRanges | Convert coordinates in underscored format to a GRanges... |

writeAsymmetricMeltedChromosomalMatrixToDisk | Write a matrix, with genes, of a submatrix of a whole genome... |

writeMeltedChromosomalMatrixToDisk | Write a matrix, with genes, of a submatrix of a whole genome... |

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