MULTIseqDemux: Demultiplex samples based on classification method from...

In satijalab/seurat: Tools for Single Cell Genomics

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)

satijalab/seurat documentation built on May 11, 2024, 4:04 a.m.