Man pages for karyotapR
DNA Copy Number Analysis for Genome-Wide Tapestri Panels
| assayBoxPlot | Generate a box plot from assay data |
| assayHeatmap | Generate heatmap of assay data |
| calcCopyNumber | Calculate relative copy number value for each cell-probe unit... |
| calcGMMCopyNumber | Call copy number for each cell-chromosome using Gaussian... |
| calcNormCounts | Normalize raw counts |
| calcSmoothCopyNumber | Smooth copy number values across chromosomes and chromosome... |
| callSampleLables | Call sample labels based on feature counts |
| corner | Print the top-left corner of a matrix |
| countBarcodedReads | Get read counts from barcoded reads |
| createTapestriExperiment | Create 'TapestriExperiment' object from Tapestri Pipeline... |
| getChrOrder | Get chromosome order from a string of chromosome/contig names |
| getCytobands | Add chromosome cytobands and chromosome arms to... |
| getGMMBoundaries | Calculate decision boundaries between components of copy... |
| getTidyData | Get tidy-style data from 'TapestriExperiment' objects |
| karyotapR-package | karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri... |
| moveNonGenomeProbes | Move non-genome probes counts and metadata to altExp slots |
| newTapestriExperimentExample | Create Example 'TapestriExperiment' |
| PCAKneePlot | Plot of PCA proportion of variance explained |
| plotCopyNumberGMM | Plot copy number GMM components |
| reducedDimPlot | Scatter plot for dimensional reduction results |
| runClustering | Cluster 2D data |
| runPCA | Cluster assay data by Principal Components Analysis |
| runUMAP | Cluster matrix data by UMAP |
| slotGettersSetters | Getter and Setter functions for 'TapestriExperiment' slots |
| TapestriExperiment-class | TapestriExperiment Class Definition |
