Man pages for navinlabcode/copykit
CopyKit
| calcConsensus | Calculate a consensus matrix of segment means based on... |
| calcInteger | calcInteger() |
| calcRatios | Calculates the ratios from a matrix of counts |
| CopyKit-class | Placeholder for the igraph class |
| data | hg38_grangeslist |
| dot-countBreakpoints | countBreakpoints |
| findAneuploidCells | findAneuploidCells |
| findClusters | Find Clusters |
| findOutliers | findOutliers() |
| findSuggestedK | findSuggestedK |
| findVariableGenes | findVariableGenes |
| inferMrca | inferMrca |
| internals | CopyKit internal functions. |
| knnSmooth | knnSmooth |
| logNorm | logNorm() |
| pipe | Pipe operator |
| plotAlluvial | plotAlluvial() |
| plotConsensusLine | plotConsensusLine |
| plotFreq | plotFreq |
| plotGeneCopy | plotGeneCopy |
| plotHeatmap | plotHeatmap |
| plotMetrics | plotMetrics |
| plotPca | plotPca |
| plotPhylo | plotPhylo() |
| plotRatio | Plot ratio |
| plotScree | plotScree |
| plotSuggestedK | plotSuggestedK |
| plotUmap | plotUmap |
| plotVariableGenes | plotVariableGenes |
| runConsensusPhylo | runConsensusPhylo |
| runCountReads | Aligns the reads from the BAM file to the variable binning... |
| runDistMat | Run distance matrix calculations |
| runMetrics | Run metrics |
| runPca | runPca() |
| runPhylo | Run phylogenetic analysis |
| runSegmentation | Run Segmentation |
| runUmap | Creates UMAP embedding |
| runVarbin | Read BAM file and perform varbin analysis |
| runVst | Variance Stabilizing Transformation |
