Creates a new musica object subsetted to only one value of a sample annotation — subset_musica_by_annotation • musicatk

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

Usage

subset_musica_by_annotation(musica, annot_col, annot_names)

Arguments

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

Value

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

Examples

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"
)