R: Identify cells matching certain criteria

WhichCells {SeuratObject} | R Documentation

## 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

### See Also

`FetchData`

### Examples

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

[Package SeuratObject version 4.1.0 Index]