Description Usage Arguments Details Value References See Also Examples
View source: R/scran_doubletCells.R
A wrapper function for scDblFinder. Identify potential doublet cells based on simulations of putative doublet expression profiles. Generate a doublet score for each cell.
1 2 3 4 5 6 7 8 9 | runDoubletCells(
inSCE,
sample = NULL,
useAssay = "counts",
nNeighbors = 50,
simDoublets = max(10000, ncol(inSCE)),
seed = 12345,
BPPARAM = BiocParallel::SerialParam()
)
|
inSCE |
A SingleCellExperiment object. |
sample |
Character vector. Indicates which sample each cell belongs to. scDblFinder will be run on cells from each sample separately. |
useAssay |
A string specifying which assay in the SCE to use. |
nNeighbors |
Number of nearest neighbors used to calculate density for doublet detection. Default 50. |
simDoublets |
Number of simulated doublets created for doublet detection. Default 10000. |
seed |
Seed for the random number generator. Default 12345. |
BPPARAM |
A |
This function is a wrapper function for scDblFinder.
runDoubletCells
runs scDblFinder for each
sample
within inSCE
iteratively. The
resulting doublet scores for all cells will be appended to the
colData of inSCE
.
A SingleCellExperiment object with the 'scran_doubletCells_score' column added to the colData slot.
Lun ATL (2018). Detecting doublet cells with scran. https://ltla.github.io/SingleCellThoughts/software/doublet_detection/bycell.html
doubletCells
1 2 3 | data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runDoubletCells(sce)
|
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