MAF {maftools} | R Documentation |
Constructor function which takes non-synonymous, and synonymous variants along with an optional clinical information and generates an MAF object
MAF(nonSyn = NULL, syn = NULL, clinicalData = NULL, verbose = TRUE)
nonSyn |
non-synonymous variants as a data.table or any object that can be coerced into a data.table (e.g: data.frame, GRanges) |
syn |
synonymous variants as a data.table or any object that can be coerced into a data.table (e.g: data.frame, GRanges) |
clinicalData |
Clinical data associated with each sample/Tumor_Sample_Barcode in MAF. Could be a text file or a data.frame. Requires at least a column with the name 'Tumor_Sample_Barcode' Default NULL. |
verbose |
Default TRUE |
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml_dt = data.table::fread(input = laml.maf) laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') #Clinical data # Just for demonstration nsyn_vars = laml_dt[Variant_Classification %in% "Missense_Mutation"] syn_vars = laml_dt[Variant_Classification %in% "Silent"] maftools::MAF(nonSyn = nsyn_vars, syn = syn_vars, clinicalData = laml.clin)