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