SeuratObject (version 5.0.2)

subset.Seurat: Subset Seurat Objects

Description

Subset Seurat Objects

Usage

# S3 method for Seurat
subset(
  x,
  subset,
  cells = NULL,
  features = NULL,
  idents = NULL,
  return.null = FALSE,
  ...
)
# S3 method for Seurat
[(x, i, j, ...)

Value

subset: A subsetted Seurat object

[: object x with features i and cells j

Arguments

x

A Seurat object

subset

Logical expression indicating features/variables to keep

cells, j

A vector of cell names or indices to keep

features, i

A vector of feature names or indices to keep

idents

A vector of identity classes to keep

return.null

If no cells are requested, return a NULL; by default, throws an error

...

Arguments passed to WhichCells

See Also

WhichCells

Seurat object, validity, and interaction methods $.Seurat(), Seurat-class, Seurat-validity, [[.Seurat(), [[<-,Seurat, [[<-,Seurat,NULL, dim.Seurat(), dimnames.Seurat(), merge.Seurat(), names.Seurat()

Examples

# `subset` examples
subset(pbmc_small, subset = MS4A1 > 4)
subset(pbmc_small, subset = `DLGAP1-AS1` > 2)
subset(pbmc_small, idents = '0', invert = TRUE)
subset(pbmc_small, subset = MS4A1 > 3, slot = 'counts')
subset(pbmc_small, features = VariableFeatures(object = pbmc_small))

# `[` examples
pbmc_small[VariableFeatures(object = pbmc_small), ]
pbmc_small[, 1:10]