GRanges_to_underscored_pos
Convert GRanges object to underscord positions.
Server component of the CNVScope plotly shiny application.
Postprocess linear regression matrix.
Assign GenomicInteractions to a predefined series of bins for row and column, corresponding to a genomic matrix.
getBlockAverageMatrixFromBreakpoints
Calculate block averages and areas in a matrix given breakpoints.
Average edges of a matrix to facilitate downsampling.
Calculate several base statistics for color rescaling.
Calculate the probability distribution of CNV concordance events with a fast kernel
Find the negative log p-value of a pair of vectors.
downsample_genomic_matrix
Rescale positive and negative data, preserving sign information.
getInterchromosomalInteractivePlot
Create an HTML widget for use in shiny or webshot for a given pair of chromosomes.
Import a breakpoint BED file.
getAsymmetricBlockIndices
Get Block Indices from an asymmetric (or symmetric) matrix.
Get the genes in the genomic ranges indicated by the row and column labels.
Rescale positive and negative data, preserving sign information.
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
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.
Runs the CNVScope plotly shiny application.
Runs the CNVScope plotly shiny application.
underscored_pos_to_GRanges
Convert coordinates in underscored format to a GRanges object.
createChromosomalMatrixSet
Create chromosomal interaction matrices for CNVScope shiny application.
formSampleMatrixFromRawGDCData
Form sample matrix from GDC copy number data files.
Create a linear regression matrix.
Read GDC segmentation datafile for low-pass sequencing data.