Function reference • karyotapR

Building `TapestriExperiment` objects

createTapestriExperiment(): Create TapestriExperiment object from Tapestri Pipeline output

show(<TapestriExperiment>): TapestriExperiment Class Definition

getChrOrder(): Get chromosome order from a string of chromosome/contig names

getCytobands(): Add chromosome cytobands and chromosome arms to TapestriExperiment

moveNonGenomeProbes(): Move non-genome probes counts and metadata to altExp slots

barcodeProbe() `barcodeProbe<-`() grnaProbe() `grnaProbe<-`() gmmParams(): Getter and Setter functions for TapestriExperiment slots

Calculate and Call Copy Number

calcCopyNumber() generateControlCopyNumberTemplate(): 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

getGMMBoundaries(): Calculate decision boundaries between components of copy number GMMs

getTidyData(): Get tidy-style data from TapestriExperiment objects

plotCopyNumberGMM(): Plot copy number GMM components

Plotting

PCAKneePlot(): Plot of PCA proportion of variance explained

assayBoxPlot(): Generate a box plot from assay data

assayHeatmap(): Generate heatmap of assay data

plotCopyNumberGMM(): Plot copy number GMM components

reducedDimPlot(): Scatter plot for dimensional reduction results

Dimensional Reduction

PCAKneePlot(): Plot of PCA proportion of variance explained

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

Handling Barcoded Reads

callSampleLables(): Call sample labels based on feature counts

countBarcodedReads() countBarcodedReadsFromContig(): Get read counts from barcoded reads

Helper and Misc Functions

corner(): Print the top-left corner of a matrix

newTapestriExperimentExample(): Create Example TapestriExperiment