.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 |