Seurat: PredictAssay – R documentation

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PredictAssay

Predict value from nearest neighbors

Description

This function will predict expression or cell embeddings from its k nearest neighbors index. For each cell, it will average its k neighbors value to get its new imputed value. It can average expression value in assays and cell embeddings from dimensional reductions.

Usage

PredictAssay(
  object,
  nn.idx,
  assay,
  reduction = NULL,
  dims = NULL,
  return.assay = TRUE,
  slot = "scale.data",
  features = NULL,
  mean.function = rowMeans,
  seed = 4273,
  verbose = TRUE
)

Arguments

`object`	The object used to calculate knn
`nn.idx`	k near neighbour indices. A cells x k matrix.
`assay`	Assay used for prediction
`reduction`	Cell embedding of the reduction used for prediction
`dims`	Number of dimensions of cell embedding
`return.assay`	Return an assay or a predicted matrix
`slot`	slot used for prediction
`features`	features used for prediction
`mean.function`	the function used to calculate row mean
`seed`	Sets the random seed to check if the nearest neighbor is query cell
`verbose`	Print progress

Value

return an assay containing predicted expression value in the data slot

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