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... |
divisors | List of Divisors |
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 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... |
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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