Get or Set SoupX Result — getSoupX<- • singleCellTK

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

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

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

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

# S4 method for 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.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
if (FALSE) {
# SoupX does not work for toy example, 
# can be tested with `sce <- importExampleData("pbmc3k")`
sce <- runSoupX(sce, sample = "sample")
soupXResults <- getSoupX(sce)
}
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
if (FALSE) {
# SoupX does not work for toy example, 
# can be tested with `sce <- importExampleData("pbmc3k")`
sce <- runSoupX(sce, sample = "sample")
soupXResults <- getSoupX(sce)
}