titv {maftools} | R Documentation |
takes output generated by read.maf and classifies Single Nucleotide Variants into Transitions and Transversions.
titv(maf, useSyn = FALSE, plot = TRUE, file = NULL)
maf |
|
useSyn |
Logical. Whether to include synonymous variants in analysis. Defaults to FALSE. |
plot |
plots a titv fractions. default TRUE. |
file |
basename for output file name. If given writes summaries to output file. Default NULL. |
list of data.frame
s with Transitions and Transversions summary.
laml.maf <- system.file("extdata", "tcga_laml.maf.gz", package = "maftools") laml <- read.maf(maf = laml.maf) laml.titv = titv(maf = laml, useSyn = TRUE)