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. |
divisors |
List of Divisors |
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. |