Demultiplex samples based on classification method from MULTI-seq (McGinnis et al., bioRxiv 2018)

Identify singlets, doublets and negative cells from multiplexing experiments. Annotate singlets by tags.

Usage

MULTIseqDemux(
  object,
  assay = "HTO",
  quantile = 0.7,
  autoThresh = FALSE,
  maxiter = 5,
  qrange = seq(from = 0.1, to = 0.9, by = 0.05),
  verbose = TRUE
)

Arguments

object: Seurat object. Assumes that the specified assay data has been added
assay: Name of the multiplexing assay (HTO by default)
quantile: The quantile to use for classification
autoThresh: Whether to perform automated threshold finding to define the best quantile. Default is FALSE
maxiter: Maximum number of iterations if autoThresh = TRUE. Default is 5
qrange: A range of possible quantile values to try if autoThresh = TRUE
verbose: Prints the output

Value

A Seurat object with demultiplexing results stored at object$MULTI_ID

References

doi:10.1038/s41592-019-0433-8

Examples

if (FALSE) { # \dontrun{
object <- MULTIseqDemux(object)
} # }