WhichCells: Identify cells matching certain criteria

In mojaveazure/seurat-object: Data Structures for Single Cell Data

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 requested, 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)

mojaveazure/seurat-object documentation built on Aug. 3, 2024, 4:59 p.m.