SubsetData: Return a subset of the Seurat object

In lambdamoses/SeuratBasics: Slimmed down version of Seurat

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 class 'Assay'
SubsetData(
  object,
  cells = NULL,
  subset.name = NULL,
  low.threshold = -Inf,
  high.threshold = Inf,
  accept.value = NULL,
  ...
)

## S3 method for class '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

## End(Not run)

lambdamoses/SeuratBasics documentation built on May 6, 2020, 9:32 a.m.