RenameCells: Rename cells

In mojaveazure/seurat-object: Data Structures for Single Cell Data

Rename cells

Description

Change the cell names in all the different parts of an object. Can be useful before combining multiple objects.

Usage

RenameCells(object, ...)

## S3 method for class 'Assay'
RenameCells(object, new.names = NULL, ...)

## S3 method for class 'Assay5'
RenameCells(object, new.names = NULL, ...)

## S3 method for class 'DimReduc'
RenameCells(object, new.names = NULL, ...)

## S3 method for class 'Neighbor'
RenameCells(object, old.names = NULL, new.names = NULL, ...)

## S3 method for class 'Seurat'
RenameCells(
  object,
  add.cell.id = missing_arg(),
  new.names = missing_arg(),
  for.merge = deprecated(),
  ...
)

Arguments

object	An object
...	Arguments passed to other methods
new.names	vector of new cell names
old.names	vector of old cell names
add.cell.id	prefix to add cell names
for.merge	Deprecated

Details

If add.cell.id is set a prefix is added to existing cell names. If new.names is set these will be used to replace existing names.

Value

An object with new cell names

Examples

# Rename cells in an Assay
head(x = colnames(x = pbmc_small[["RNA"]]))
renamed.assay <- RenameCells(
    pbmc_small[["RNA"]],
    new.names = paste0("A_", colnames(x = pbmc_small[["RNA"]]))
)
head(x = colnames(x = renamed.assay))

# Rename cells in a DimReduc
head(x = Cells(x = pbmc_small[["pca"]]))
renamed.dimreduc <- RenameCells(
    object = pbmc_small[["pca"]],
    new.names = paste0("A_", Cells(x = pbmc_small[["pca"]]))
)
head(x = Cells(x = renamed.dimreduc))

# Rename cells in a Seurat object
head(x = colnames(x = pbmc_small))
pbmc_small <- RenameCells(object = pbmc_small, add.cell.id = "A")
head(x = colnames(x = pbmc_small))

mojaveazure/seurat-object documentation built on Dec. 13, 2024, 9:23 a.m.