Seurat (version 2.3.1)

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, ect..

Usage

WhichCells(object, ident = NULL, ident.remove = NULL, cells.use = NULL,
  subset.name = NULL, accept.low = -Inf, accept.high = Inf,
  accept.value = NULL, max.cells.per.ident = Inf, random.seed = 1, ...)

Arguments

object

Seurat object

ident

Identity classes to subset. Default is all identities.

ident.remove

Indentity classes to remove. Default is NULL.

cells.use

Subset of cell names

subset.name

Parameter to subset on. Eg, the name of a gene, PC1, a column name in [e-mail], etc. Any argument that can be retreived using FetchData

accept.low

Low cutoff for the parameter (default is -Inf)

accept.high

High cutoff for the parameter (default is Inf)

accept.value

Returns all cells with the subset name equal to this value

max.cells.per.ident

Can be used to downsample the data to a certain max per cell ident. Default is INF.

random.seed

Random seed for downsampling

…

Additional arguments to be passed to FetchData (for example, use.imputed=TRUE)

Value

A vector of cell names

Examples

# NOT RUN {
WhichCells(object = pbmc_small, ident = 2)

# }