Seurat (version 3.1.1)

SubsetData: Return a subset of the Seurat object

Description

Creates a Seurat object containing only a subset of the cells in the original object. Takes either a list of cells to use as a subset, or a parameter (for example, a gene), to subset on.

Usage

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

Arguments

object

An object

...

Arguments passed to other methods

cells

A vector of cell names to use as a subset. If NULL (default), then this list will be computed based on the next three arguments. Otherwise, will return an object consissting only of these cells

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 cells with the subset name equal to this value

assay

Assay to subset on

ident.use

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

Value

Returns a Seurat object containing only the relevant subset of cells

Examples

# NOT RUN {
pbmc1 <- SubsetData(object = pbmc_small, cells = colnames(x = pbmc_small)[1:40])
pbmc1
# }
# NOT RUN {
# }