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

Value

A vector of cell names

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

Examples

Run this code

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

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