slotGettersSetters: Getter and Setter functions for 'TapestriExperiment' slots

In karyotapR: DNA Copy Number Analysis for Genome-Wide Tapestri Panels

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 signature 'TapestriExperiment'
barcodeProbe(x)

barcodeProbe(x) <- value

## S4 replacement method for signature 'TapestriExperiment'
barcodeProbe(x) <- value

grnaProbe(x)

## S4 method for signature 'TapestriExperiment'
grnaProbe(x)

grnaProbe(x) <- value

## S4 replacement method for signature 'TapestriExperiment'
grnaProbe(x) <- value

gmmParams(x)

## S4 method for signature 'TapestriExperiment'
gmmParams(x)

Arguments

x	A TapestriExperiment object
value	Character, probe ID to assign to slot
TapestriExperiment	A TapestriExperiment object

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.

Functions

• barcodeProbe(TapestriExperiment): barcodeProbe getter

• barcodeProbe(TapestriExperiment) <- value: barcodeProbe setter

• grnaProbe(TapestriExperiment): grnaProbe getter

• grnaProbe(TapestriExperiment) <- value: grnaProbe setter

• gmmParams(TapestriExperiment): gmmParams getter

Examples

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

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

gmmParams(tap.object)

karyotapR documentation built on Sept. 8, 2023, 5:07 p.m.