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MULTIseqDemux

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

Examples

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

## End(Not run)
Seurat

Tools for Single Cell Genomics

v4.0.1
GPL-3 | file LICENSE
Authors
Andrew Butler [ctb] (<https://orcid.org/0000-0003-3608-0463>), Saket Choudhary [ctb] (<https://orcid.org/0000-0001-5202-7633>), Charlotte Darby [ctb] (<https://orcid.org/0000-0003-2195-5300>), Jeff Farrell [ctb], Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Jaison Jain [ctb] (<https://orcid.org/0000-0002-9478-5018>), Efthymia Papalexi [ctb] (<https://orcid.org/0000-0001-5898-694X>), Patrick Roelli [ctb], Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>), Karthik Shekhar [ctb], Avi Srivastava [ctb] (<https://orcid.org/0000-0001-9798-2079>), Tim Stuart [ctb] (<https://orcid.org/0000-0002-3044-0897>), Kristof Torkenczy [ctb] (<https://orcid.org/0000-0002-4869-7957>), Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Satija Lab and Collaborators [fnd]
Initial release
2021-03-17

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