subset_musica_by_annotation: Creates a new musica object subsetted to only one value of a...
In musicatk: Mutational Signature Comprehensive Analysis Toolkit

Description Usage Arguments Value Examples

Creates a new musica object subsetted to only one value of a sample annotation

1	subset_musica_by_annotation(musica, annot_col, annot_names)

`musica`	A `musica` object.
`annot_col`	Annotation class to use for subsetting
`annot_names`	Annotational value to subset to

Returns a new musica object with sample annotations, count tables, and variants subsetted to only contains samples of the specified annotation type

data(musica_sbs96)
annot <- read.table(system.file("extdata", "sample_annotations.txt", 
package = "musicatk"), sep = "\t", header=TRUE)

samp_annot(musica_sbs96, "Tumor_Subtypes") <- annot$Tumor_Subtypes

musica_sbs96 <- subset_musica_by_annotation(musica_sbs96, "Tumor_Subtypes", 
"Lung")