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Seurat (version 3.1.4)

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 object@meta.data, 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

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

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