MULTIseqDemux {Seurat}

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

Description

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

https://www.biorxiv.org/content/10.1101/387241v1

Examples

## Not run: 
object <- MULTIseqDemux(object)

## End(Not run)