R/scds_doubletdetection.R
runCxdsBcdsHybrid.Rd
A wrapper function for cxds_bcds_hybrid. Annotate
doublets/multiplets using a binary classification approach to discriminate
artificial doublets from original data. Generate a doublet
score for each cell. Infer doublets if estNdbl
is TRUE
.
A SingleCellExperiment object.
Needs counts
in assays slot.
Character vector. Indicates which sample each cell belongs to. cxds_bcds_hybrid will be run on cells from each sample separately. If NULL, then all cells will be processed together. Default NULL.
Seed for the random number generator. Default 12345.
The number of top varialbe genes to consider. Used in both csds
and bcds
. Default 500
.
See cxds_bcds_hybrid for more information. Default NULL
.
See cxds_bcds_hybrid for more information. Default NULL
.
See cxds_bcds_hybrid for more information. Default FALSE
.
See cxds_bcds_hybrid for more information. Default FALSE
.
See cxds_bcds_hybrid for more information. Default FALSE
.
A string specifying which assay in the SCE to use.
A SingleCellExperiment object with
cxds_bcds_hybrid output appended to the
colData slot. The columns include
hybrid_score and optionally hybrid_call. Please refer to the documentation of cxds_bcds_hybrid for details.
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runCxdsBcdsHybrid(sce)
#> Sat Mar 18 10:30:31 2023 ... Running 'cxds_bcds_hybrid'