R/methods.R
samp_annot.Rd
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.
samp_annot(object) # S4 method for musica samp_annot(object) # S4 method for musica_result samp_annot(object) 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
object | A |
---|---|
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. |
A new object with the sample annotations added to the table in the
sample_annotations
slot.
See sample_names
to get a vector of sample names in
the musica
or musica_result
object.
#> 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