runCellQC {singleCellTK} | R Documentation |
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", "scrublet", "doubletFinder", "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", "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'") ## Not run: sce <- runCellQC(sce) ## End(Not run)