# DNA Copy Number Analysis for Genome-Wide Tapestri Panels

## Documentation for package ‘karyotapR’ version 1.0.1

- DESCRIPTION file.
- Package NEWS.

## Help Pages

.TapestriExperiment | TapestriExperiment Class Definition
assayBoxPlot | Generate a box plot from assay data
assayHeatmap | Generate heatmap of assay data
barcodeProbe | Getter and Setter functions for 'TapestriExperiment' slots
barcodeProbe-method | Getter and Setter functions for 'TapestriExperiment' slots
barcodeProbe<- | Getter and Setter functions for 'TapestriExperiment' slots
barcodeProbe<--method | Getter and Setter functions for 'TapestriExperiment' slots
calcCopyNumber | Calculate relative copy number value for each cell-probe unit using reference sample
calcGMMCopyNumber | Call copy number for each cell-chromosome using Gaussian mixture models
calcNormCounts | Normalize raw counts
calcSmoothCopyNumber | Smooth copy number values across chromosomes and chromosome arms
callSampleLables | Call sample labels based on feature counts
corner | Print the top-left corner of a matrix
countBarcodedReads | Get read counts from barcoded reads
countBarcodedReadsFromContig | Get read counts from barcoded reads
createTapestriExperiment | Create 'TapestriExperiment' object from Tapestri Pipeline output
Custom Slot Getters and Setters | Getter and Setter functions for 'TapestriExperiment' slots
generateControlCopyNumberTemplate | Calculate relative copy number value for each cell-probe unit using reference sample
getChrOrder | Get chromosome order from a string of chromosome/contig names
getCytobands | Add chromosome cytobands and chromosome arms to 'TapestriExperiment'
getGMMBoundaries | Calculate decision boundaries between components of copy number GMMs
getTidyData | Get tidy-style data from 'TapestriExperiment' objects
gmmParams | Getter and Setter functions for 'TapestriExperiment' slots
gmmParams-method | Getter and Setter functions for 'TapestriExperiment' slots
grnaProbe | Getter and Setter functions for 'TapestriExperiment' slots
grnaProbe-method | Getter and Setter functions for 'TapestriExperiment' slots
grnaProbe<- | Getter and Setter functions for 'TapestriExperiment' slots
grnaProbe<--method | Getter and Setter functions for 'TapestriExperiment' slots
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
show-method | TapestriExperiment Class Definition
TapestriExperiment-class | TapestriExperiment Class Definition