Run DoubletFinder on a Seurat object
Usage
RunSeuratDoubletFinder(
object,
ident = NULL,
ncores = 1,
PCs = 30,
pN = 0.25,
doublets = 0.075,
reuse.pANN = NULL,
log = NULL,
allow_warnings = FALSE
)Arguments
- object
Seurat object
- ident
Cluster identity to use for homotypic doublet proportion estimation. If NULL or not exists, will run clustering first to get cluster identities.
- ncores
Number of cores to use
- PCs
Number of statistically-significant principal components
- pN
The number of generated artificial doublets, expressed as a proportion of the merged real-artificial data. Default is set to 0.25, based on observation that DoubletFinder performance is largely pN-invariant (see McGinnis, Murrow and Gartner 2019, Cell Systems).
- doublets
The expected proportion of doublets in the dataset. Default is set to 0.075
- reuse.pANN
Metadata column name for previously-generated pANN results. If NULL (default), an existing pANN column matching the current pN/pK is reused to skip pANN computation, if available. Set to FALSE or an invalid column name is treated as NULL with a warning.