R/doubletFinder_doubletDetection.R
runDoubletFinder.Rd
Uses doubletFinder to determine cells within the dataset suspected to be doublets.
runDoubletFinder(
inSCE,
useAssay = "counts",
sample = NULL,
seed = 12345,
seuratNfeatures = 2000,
seuratPcs = seq(15),
seuratRes = 1.5,
formationRate = 0.075,
nCores = NULL,
verbose = FALSE
)
Input SingleCellExperiment object. Must contain a counts matrix
Indicate which assay to use. Default "counts".
Numeric vector. Each cell will be assigned a sample number.
Seed for the random number generator. Default 12345.
Integer. Number of highly variable genes to use. Default 2000.
Numeric vector. The PCs used in seurat function to determine number of clusters. Default 1:15.
Numeric vector. The resolution parameter used in seurat, which adjusts the number of clusters determined via the algorithm. Default 1.5.
Doublet formation rate used within algorithm. Default 0.075.
Number of cores used for running the function.
Boolean. Wheter to print messages from Seurat and DoubletFinder. Default FALSE.
SingleCellExperiment object containing the 'doublet_finder_doublet_score'.
data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- runDoubletFinder(sce)
#> Thu Apr 28 11:27:56 2022 ... Running 'doubletFinder'