Man pages for jamesdalg/CNVScope
A Versatile Toolkit for Copy Number Variation Relationship Data Analysis and Visualization

averageMatrixEdgesAverage edges of a matrix to facilitate downsampling.
calcCNVKernelProbDistCalculate the probability distribution of CNV concordance...
calcVecLMsCreate a linear regression matrix.
CNVScopeserverServer component of the CNVScope plotly shiny application.
createChromosomalMatrixSetCreate chromosomal interaction matrices for CNVScope shiny...
downsample_genomic_matrixRescale positive and negative data, preserving sign...
extractNegLogPvalFind the negative log p-value of a pair of vectors.
formSampleMatrixFromRawGDCDataForm sample matrix from GDC low-pass segmentation datafiles.
freadGDCfileRead GDC segmentation datafile for low-pass sequencing data.
getAnnotationMatrixGet the genes in the genomic ranges indicated by the row and...
getAsymmetricBlockIndicesGet Block Indices from an asymmetric (or symmetric) matrix.
getBlockAverageMatrixFromBreakpointsCalculate block averages and areas in a matrix given...
getGlobalRescalingStatsCalculate several base statistics for color rescaling.
getInterchromosomalInteractivePlotCreate an HTML widget for use in shiny or webshot for a given...
GRanges_to_underscored_posConvert GRanges object to underscord positions.
importBreakpointBedImport a breakpoint BED file.
matheadGets a small piece of a matrix (top left corner) for viewing,...
nbl_result_matrix_sign_smallNeuroblastoma sample CNV relationship matrix
postProcessLinRegMatrixPostprocess linear regression matrix.
rebinGenomicInteractionsAssign GenomicInteractions to a predefined series of bins for...
runCNVScopeLocalRuns the CNVScope plotly shiny application.
runCNVScopeShinyRuns the CNVScope plotly shiny application.
signedRescaleRescale positive and negative data, preserving sign...
underscored_pos_to_GRangesConvert coordinates in underscored format to a GRanges...
writeAsymmetricMeltedChromosomalMatrixToDiskWrite a matrix, with genes, of a submatrix of a whole genome...
writeMeltedChromosomalMatrixToDiskWrite a matrix, with genes, of a submatrix of a whole genome...
jamesdalg/CNVScope documentation built on July 21, 2019, 9:36 a.m.