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