DNA Copy Number Analysis for Genome-Wide Tapestri Panels

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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