R/main_class.R
subset_musica_by_annotation.Rd
Creates a new musica object subsetted to only one value of a sample annotation
subset_musica_by_annotation(musica, annot_col, annot_names)
musica | A |
---|---|
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")