A wrapper function for cxds. Annotate
doublets/multiplets using co-expression based approach. Generate a doublet
score for each cell. Infer doublets if estNdbl
is TRUE
.
runCxds( inSCE, sample = NULL, seed = 12345, ntop = 500, binThresh = 0, verb = FALSE, retRes = FALSE, estNdbl = FALSE, useAssay = "counts" )
inSCE | A SingleCellExperiment object.
Needs |
---|---|
sample | Character vector. Indicates which sample each cell belongs to. cxds will be run on cells from each sample separately. If NULL, then all cells will be processed together. Default NULL. |
seed | Seed for the random number generator. Default 12345. |
ntop | See cxds for more information. Default |
binThresh | See cxds for more information. Default |
verb | See cxds for more information. Default |
retRes | See cxds for more information. Default |
estNdbl | See cxds for more information. Default |
useAssay | A string specifying which assay in the SCE to use. |
A SingleCellExperiment object with cxds output appended to the colData slot. The columns include cxds_score and optionally cxds_call. Please refer to the documentation of cxds for details.
data(scExample, package = "singleCellTK") sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") sce <- runCxds(sce)#>