Seurat (version 3.1.1)

OldWhichCells: 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

OldWhichCells(object, ...)
# S3 method for Assay
OldWhichCells(object, cells, subset.name = NULL,
  low.threshold = -Inf, high.threshold = Inf, accept.value = NULL,
  ...)
# S3 method for Seurat
OldWhichCells(object, cells = NULL,
  subset.name = NULL, low.threshold = -Inf, high.threshold = Inf,
  accept.value = NULL, ident.keep = NULL, ident.remove = NULL,
  max.cells.per.ident = Inf, random.seed = 1, assay = NULL, ...)

Arguments

object

An object

...

Arguments passed to other methods and FetchData

cells

Subset of cell names

subset.name

Parameter to subset on. Eg, the name of a gene, PC_1, a column name in [e-mail], etc. Any argument that can be retreived using FetchData

low.threshold

Low cutoff for the parameter (default is -Inf)

high.threshold

High cutoff for the parameter (default is Inf)

accept.value

Returns all cells with the subset name equal to this value

ident.keep

Create a cell subset based on the provided identity classes

ident.remove

Subtract out cells from these identity classes (used for filtration)

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

assay

Which assay to filter on

Value

A vector of cell names

See Also

FetchData

Examples

# NOT RUN {
OldWhichCells(object = pbmc_small, ident.keep = 2)
# }
# NOT RUN {
# }