samp_annot {musicatk} | R Documentation

## Get or set sample annotations from a musica or musica_result object

### Description

Sample annotations can be used to store information about each sample such as tumor type or treatment status. These are used in downstream plotting functions such as `plot_exposures` or `plot_umap` to group or color samples by a particular annotation.

### Usage

    samp_annot(object)

    ## S4 method for signature 'musica'
    samp_annot(object)

    ## S4 method for signature 'musica_result'
    samp_annot(object)

    samp_annot(object, name) <- value

    ## S4 replacement method for signature 'musica,character,vector'
    samp_annot(object, name) <- value

    ## S4 replacement method for signature 'musica_result,character,vector'
    samp_annot(object, name) <- value

### Arguments

`object` | A `musica` object generated by the create_musica function or a `musica_result` object generated by a mutational discovery or prediction tool.
`name` | The name of the new annotation to add.
`value` | A vector containing the new sample annotations. Needs to be the same length as the number of samples in the object.

### Value

A new object with the sample annotations added to the table in the `sample_annotations` slot.

### See Also

See `sample_names` to get a vector of sample names in the `musica` or `musica_result` object.

### Examples

    data(res_annot)
    samp_annot(res_annot)

    # Add new annotation
    samp_annot(res_annot, "New_Annotation") <- rep(c("A", "B"), c(3, 4))
    samp_annot(res_annot)
    data(musica)
    samp_annot(musica, "example") <- rep("ex", 7)

[Package musicatk version 1.2.0 Index]