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, cells.use = NULL, subset.name = NULL, ident.use = NULL,
  accept.low = -Inf, accept.high = Inf, do.center = F, do.scale = F,
  max.cells.per.ident = Inf, random.seed = 1, ...)

Arguments

object

Seurat object

cells.use

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, PC1, a column name in object@data.info, etc. Any argument that can be retreived using FetchData

ident.use

Create a cell subset based on the provided identity classes

accept.low

Low cutoff for the parameter (default is -Inf)

accept.high

High cutoff for the parameter (default is Inf)

do.center

Recenter the new object@scale.data

do.scale

Rescale the new object@scale.data. FALSE by default

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)