Seurat (version 1.2.1)

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, cells.use = NULL, subset.name = NULL, accept.low = -Inf, accept.high = Inf, do.center = TRUE, do.scale = TRUE, ...)

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 [e-mail], etc. Any argument that can be retreived using fetch.data

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 [e-mail]

do.scale

Rescale the new [e-mail]

...

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

Value

Returns a Seurat object containing only the relevant subset of cells