SeuratObject: WhichCells – R documentation

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WhichCells

Identify cells matching certain criteria

Description

Returns a list of cells that match a particular set of criteria such as identity class, high/low values for particular PCs, etc.

Usage

WhichCells(object, ...)

## S3 method for class 'Assay'
WhichCells(object, cells = NULL, expression, invert = FALSE, ...)

## S3 method for class 'Seurat'
WhichCells(
  object,
  cells = NULL,
  idents = NULL,
  expression,
  slot = "data",
  invert = FALSE,
  downsample = Inf,
  seed = 1,
  ...
)

Arguments

`object`	An object
`...`	Arguments passed on to `CellsByIdentities` `return.null` If no cells are request, return a `NULL`; by default, throws an error
`cells`	Subset of cell names
`expression`	A predicate expression for feature/variable expression, can evaluate anything that can be pulled by `FetchData`; please note, you may need to wrap feature names in backticks (``) if dashes between numbers are present in the feature name
`invert`	Invert the selection of cells
`idents`	A vector of identity classes to keep
`slot`	Slot to pull feature data for
`downsample`	Maximum number of cells per identity class, default is `Inf`; downsampling will happen after all other operations, including inverting the cell selection
`seed`	Random seed for downsampling. If NULL, does not set a seed

Value

A vector of cell names

Examples

WhichCells(pbmc_small, idents = 2)
WhichCells(pbmc_small, expression = MS4A1 > 3)
levels(pbmc_small)
WhichCells(pbmc_small, idents = c(1, 2), invert = TRUE)

SeuratObject

Data Structures for Single Cell Data

v4.0.1

GPL-3

Authors

Rahul Satija [aut] (<https://orcid.org/0000-0001-9448-8833>), Andrew Butler [aut] (<https://orcid.org/0000-0003-3608-0463>), Paul Hoffman [aut, cre] (<https://orcid.org/0000-0002-7693-8957>), Tim Stuart [aut] (<https://orcid.org/0000-0002-3044-0897>), Jeff Farrell [ctb], Shiwei Zheng [ctb] (<https://orcid.org/0000-0001-6682-6743>), Christoph Hafemeister [ctb] (<https://orcid.org/0000-0001-6365-8254>), Patrick Roelli [ctb], Yuhan Hao [ctb] (<https://orcid.org/0000-0002-1810-0822>)

Initial release

2021-05-07