View source: R/scds_doubletdetection.R
runCxds | R Documentation |
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. |
sample |
Character vector or colData variable name. Indicates which
sample each cell belongs to. Default |
seed |
Seed for the random number generator, can be |
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. Default
|
When the argument sample
is specified, cxds will
be run on cells from each sample separately. If sample = NULL
, then
all cells will be processed together.
A SingleCellExperiment object with cxds output appended to the colData slot. The columns include cxds_score and optionally cxds_call.
cxds
, plotCxdsResults
,
runCellQC
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runCxds(sce)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.