Function to generate silent and non-silent mutation plot

This function generates silent and non-silent mutation plot using the MAF data.

generateMutationTypePlot(mymaf, savename = NULL, returndata = FALSE)

Arguments

mymaf

The MAF object

savename

The name and path of the output file

returndata

Flag to output the plot data (By Default returndata = FALSE)

Value

A ggplot object if returndata is FALSE or a list containing the ggplot object and plot data if returndata is TRUE

Author

Mayank Tandon, Ashish Jain

Examples

library(MAFDash)
library(maftools)
maf <- system.file("extdata", "test.mutect2.maf.gz", package = "MAFDash")
generateMutationTypePlot(read.maf(maf))
#> -Reading
#> -Validating
#> -Silent variants: 561 
#> -Summarizing
#> --Possible FLAGS among top ten genes:
#>   MACF1
#>   MUC16
#> -Processing clinical data
#> --Missing clinical data
#> -Finished in 0.242s elapsed (0.222s cpu)