getSoupX: Get or Set SoupX Result

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Get or Set SoupX Result

Description

S4 method for getting and setting SoupX results that cannot be appended to either rowData(inSCE) or colData(inSCE).

S4 method for getting and setting SoupX results that cannot be appended to either rowData(inSCE) or colData(inSCE).

Usage

getSoupX(inSCE, sampleID, background = FALSE) <- value

getSoupX(inSCE, sampleID = NULL, background = FALSE)

## S4 method for signature 'SingleCellExperiment'
getSoupX(inSCE, sampleID = NULL, background = FALSE)

## S4 replacement method for signature 'SingleCellExperiment'
getSoupX(inSCE, sampleID, background = FALSE) <- value

Arguments

inSCE	A SingleCellExperiment object. For getter method, runSoupX must have been already applied.
sampleID	Character vector. For getter method, the samples that should be included in the returned list. Leave this NULL for all samples. Default NULL. For setter method, only one sample allowed.
background	Logical. Whether background was applied when running runSoupX. Default FALSE.
value	Dedicated list object of SoupX results.

Value

For getter method, a list with SoupX results for specified samples. For setter method, inSCE with SoupX results updated.

For getter method, a list with SoupX results for specified samples. For setter method, inSCE with SoupX results updated.

See Also

runSoupX, plotSoupXResults

Examples

## Not run: 
sce <- importExampleData("pbmc3k")
sce <- runSoupX(sce, sample = "sample")
soupXResults <- getSoupX(sce)

## End(Not run)

compbiomed/singleCellTK documentation built on June 11, 2025, 9:45 a.m.