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.


# S4 method for musica

# S4 method for musica_result

samp_annot(object, name) <- value

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

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



A musica object generated by the create_musica function or a musica_result object generated by a mutational discovery or prediction tool.


The name of the new annotation to add.


A vector containing the new sample annotations. Needs to be the same length as the number of samples in the object.


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.


data(res_annot) samp_annot(res_annot)
#> Samples Tumor_Subtypes #> 1: TCGA-94-7557-01A-11D-2122-08 Lung #> 2: TCGA-56-7582-01A-11D-2042-08 Lung #> 3: TCGA-77-7335-01A-11D-2042-08 Lung #> 4: TCGA-97-7938-01A-11D-2167-08 Lung #> 5: TCGA-EE-A3J5-06A-11D-A20D-08 Breast #> 6: TCGA-ER-A197-06A-32D-A197-08 Breast #> 7: TCGA-ER-A19O-06A-11D-A197-08 Breast
# Add new annotation samp_annot(res_annot, "New_Annotation") <- rep(c("A", "B"), c(3, 4)) samp_annot(res_annot)
#> Samples Tumor_Subtypes New_Annotation #> 1: TCGA-94-7557-01A-11D-2122-08 Lung A #> 2: TCGA-56-7582-01A-11D-2042-08 Lung A #> 3: TCGA-77-7335-01A-11D-2042-08 Lung A #> 4: TCGA-97-7938-01A-11D-2167-08 Lung B #> 5: TCGA-EE-A3J5-06A-11D-A20D-08 Breast B #> 6: TCGA-ER-A197-06A-32D-A197-08 Breast B #> 7: TCGA-ER-A19O-06A-11D-A197-08 Breast B
data(musica) samp_annot(musica, "example") <- rep("ex", 7)