WhichCells: Identify cells matching certain criteria

In atakanekiz/Seurat3.0: Tools for Single Cell Genomics

Description

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

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, invert = FALSE, downsample = Inf, seed = 1, ...)

Arguments

object	An object
...	Arguments passed to other methods
cells	Subset of cell names
expression	A predicate expression for feature/variable expression, can evalue anything that can be pulled by FetchData
invert	Invert the selection of cells
idents	A vector of identity classes to keep
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

Value

A vector of cell names

See Also

FetchData

Examples

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

atakanekiz/Seurat3.0 documentation built on May 26, 2019, 2:33 a.m.