Run emptyDrops on the count matrix in the provided \linkS4classSingleCellExperiment object. Distinguish between droplets containing cells and ambient RNA in a droplet-based single-cell RNA sequencing experiment.
runEmptyDrops(
inSCE,
sample = NULL,
useAssay = "counts",
lower = 100,
niters = 10000,
testAmbient = FALSE,
ignore = NULL,
alpha = NULL,
retain = NULL,
barcodeArgs = list(),
BPPARAM = BiocParallel::SerialParam()
)
A SingleCellExperiment object. Must contain a raw counts matrix before empty droplets have been removed.
Character vector or colData variable name. Indicates which
sample each cell belongs to. Default NULL
.
A string specifying which assay in the SCE to use. Default
"counts"
See emptyDrops for more information.
Default 100
.
See emptyDrops for more information.
Default 10000
.
See emptyDrops for more information.
Default FALSE
.
See emptyDrops for more information.
Default NULL
.
See emptyDrops for more information.
Default NULL
.
See emptyDrops for more information.
Default NULL
.
See emptyDrops for more information.
Default list()
.
See emptyDrops for more information.
Default BiocParallel::SerialParam()
.
A SingleCellExperiment object with the
emptyDrops output table appended to the
colData slot. The columns include
emptyDrops_total
, emptyDrops_logprob
,
emptyDrops_pvalue
, emptyDrops_limited
, emptyDrops_fdr
.
Please refer to the documentation of emptyDrops for
details.
data(scExample, package = "singleCellTK")
sce <- runEmptyDrops(inSCE = sce)
#> Mon Dec 19 18:09:44 2022 ... Running 'emptyDrops'