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karyotapR (version 1.0.1)

Custom Slot Getters and Setters: Getter and Setter functions for TapestriExperiment slots

Description

Get and set custom slots in TapestriExperiment. Slots include barcodeProbe for a sample barcode probe ID and grnaProbe for a gRNA-associated probe ID. These are used as shortcuts for moveNonGenomeProbes() and countBarcodedReads(). gmmParams holds parameters and metadata for GMM copy number calling models.

Usage

barcodeProbe(x)
# S4 method for TapestriExperiment
barcodeProbe(x)
barcodeProbe(x) <- value
# S4 method for TapestriExperiment
barcodeProbe(x) <- value
grnaProbe(x)
# S4 method for TapestriExperiment
grnaProbe(x)
grnaProbe(x) <- value
# S4 method for TapestriExperiment
grnaProbe(x) <- value
gmmParams(x)
# S4 method for TapestriExperiment
gmmParams(x)

Value

For the getter methods barcodeProbe, grnaProbe, and gmmParams, the value of the given slot is returned. For the setter methods barcodeProbe and grnaProbe, a TapestriExperiment object is returned with modifications made to the given slot.

Arguments

x

A TapestriExperiment object

value

Character, probe ID to assign to slot

TapestriExperiment

A TapestriExperiment object

Functions

  • barcodeProbe(TapestriExperiment): barcodeProbe getter

  • barcodeProbe(TapestriExperiment) <- value: barcodeProbe setter

  • grnaProbe(TapestriExperiment): grnaProbe getter

  • grnaProbe(TapestriExperiment) <- value: grnaProbe setter

  • gmmParams(TapestriExperiment): gmmParams getter

Examples

Run this code
tap.object <- newTapestriExperimentExample() # example TapestriExperiment object
barcodeProbe(tap.object) <- "Probe01"
barcodeProbe(tap.object)

grnaProbe(tap.object) <- "Probe02"
grnaProbe(tap.object)

gmmParams(tap.object)

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