R: Rename cells

RenameCells {SeuratObject} | R Documentation

## 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 '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 = NULL,
      new.names = NULL,
      for.merge = FALSE,
      ...
    )

### 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` | Only rename slots needed for merging Seurat objects. Currently only renames the raw.data and meta.data slots.

### 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))

[Package SeuratObject version 4.0.3 Index]