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

calcCNVKernelProbDist |
Calculate the probability distribution of CNV concordance events with a fast kernel |

calcVecLMs |
Create a linear regression matrix. |

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

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

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

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

formSampleMatrixFromRawGDCData |
Form sample matrix from GDC copy number data files. |

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

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

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

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

getGlobalRescalingStats |
Calculate several base statistics for color rescaling. |

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

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, rather than pulling the first n rows. |

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 row and column, corresponding to a genomic matrix. |

runCNVScopeLocal |
Runs the CNVScope plotly shiny application. |

runCNVScopeShiny |
Runs the CNVScope plotly shiny application. |

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

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

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

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