cData {MAST} | R Documentation

## Deprecated cell/feature data accessors/mutators

### Description

These functions are now all deprecated and will be removed in a future release.

### Usage

    cData(sc)

    cData(sc) <- value

    ## S4 method for signature 'SingleCellAssay'
    cData(sc)

    ## S4 replacement method for signature 'SingleCellAssay'
    cData(sc) <- value

    ## S4 method for signature 'SingleCellAssay,SingleCellAssay'
    combine(x, y, ...)

    ## S4 method for signature 'SingleCellAssay,ANY'
    combine(x, y, ...)

### Arguments

`sc` | An object with `cellData`
`value` | replacement value
`x` | `SingleCellAssay`
`y` | `SingleCellAssay`
`...` | `SingleCellAssay`

### Details

`cData(sc)`: Return the `cellData` `data.frame`.

`cData(sc)<-value`: Replace the cellData with `value`, which can be either an `AnnotatedDataFrame` or `data.frame`. The replacement is checked that it has mandatory fields defined by its class.

`combine(x, y, ...)`: Concatenate two experiments along rows/columns

### Value

`DataFrame` or modifies the `SingleCellAssay` object in place

### Replacement Functions

You should transition to use the following replacements:

`cData`

  colData

`fData`

  mcols

`exprs`

  assay

`combine`

  cbind2 or rbind2

### See Also

exprs

### Examples

    data(vbetaFA)
    stopifnot(all.equal(hushWarning(cData(vbetaFA), 'deprecated'),colData(vbetaFA)))
    stopifnot(all.equal(hushWarning(fData(vbetaFA), 'deprecated'), mcols(vbetaFA)))
    stopifnot(all.equal(hushWarning(exprs(vbetaFA), 'deprecated'), t(assay(vbetaFA))))

[Package MAST version 1.4.1 Index]