A wrapper function to run several QC algorithms on a SingleCellExperiment object containing cells after empty droplets have been removed.
runCellQC( inSCE, algorithms = c("QCMetrics", "scDblFinder", "cxds", "bcds", "cxds_bcds_hybrid", "decontX"), sample = NULL, collectionName = NULL, geneSetList = NULL, geneSetListLocation = "rownames", geneSetCollection = NULL, useAssay = "counts", seed = 12345, paramsList = NULL )
inSCE | A SingleCellExperiment object. |
---|---|
algorithms | Character vector. Specify which QC algorithms to run. Available options are "QCMetrics", "scrublet", "doubletFinder", "scDblFinder", "cxds", "bcds", "cxds_bcds_hybrid", and "decontX". |
sample | Character vector. Indicates which sample each cell belongs to. Algorithms will be run on cells from each sample separately. |
collectionName | Character. Name of a |
geneSetList | See |
geneSetListLocation | See |
geneSetCollection | See |
useAssay | A string specifying which assay contains the count matrix for cells. |
seed | Seed for the random number generator. Default 12345. |
paramsList | A list containing parameters for QC functions. Default NULL. |
SingleCellExperiment object containing the outputs of the
specified algorithms in the colData
of inSCE
.
data(scExample, package = "singleCellTK") sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") if (FALSE) { sce <- runCellQC(sce) }