Seurat: MapQuery – R documentation

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MapQuery

Map query cells to a reference

Description

This is a convenience wrapper function around the following three functions that are often run together when mapping query data to a reference: TransferData, IntegrateEmbeddings, ProjectUMAP.

Usage

MapQuery(
  anchorset,
  query,
  reference,
  refdata = NULL,
  new.reduction.name = NULL,
  reference.reduction = NULL,
  reduction.model = NULL,
  transferdata.args = list(),
  integrateembeddings.args = list(),
  projectumap.args = list(),
  verbose = TRUE
)

Arguments

`anchorset`	An AnchorSet object
`query`	Query object used in anchorset construction
`reference`	Reference object used in anchorset construction
`refdata`	Data to transfer. This can be specified in one of two ways: The reference data itself as either a vector where the names correspond to the reference cells, or a matrix, where the column names correspond to the reference cells. The name of the metadata field or assay from the reference object provided. This requires the reference parameter to be specified. If pulling assay data in this manner, it will pull the data from the data slot. To transfer data from other slots, please pull the data explicitly with `GetAssayData` and provide that matrix here.
`new.reduction.name`	Name for new integrated dimensional reduction.
`reference.reduction`	Name of reduction to use from the reference for neighbor finding
`reduction.model`	`DimReduc` object that contains the umap model
`transferdata.args`	A named list of additional arguments to `TransferData`
`integrateembeddings.args`	A named list of additional arguments to `IntegrateEmbeddings`
`projectumap.args`	A named list of additional arguments to `ProjectUMAP`
`verbose`	Print progress bars and output

Value

Returns a modified query Seurat object containing new Assays corresponding to the features transferred and/or their corresponding prediction scores from TransferData. An integrated reduction from IntegrateEmbeddings. And an projected umap reduction of the query cells projected into the reference umap.

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