I am trying to do somatic variation analysis using TCGABiolinks package in R 3.6.
I want to use hg19 version of human genome. However I could not find any way to visualize the results using Maftools. It seems Maftools has only been designed for hg38.
The following is the punch of codes I used for data visualization by Maftools:
library(maftools) library(dplyr) maf <- GDCquery_Maf("KIRP", pipelines = "mutect") %>% read.maf datatable(getSampleSummary(maf), filter = 'top', options = list(scrollX = TRUE, keys = TRUE, pageLength = 5000), rownames = FALSE) plotmafSummary(maf = maf, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE) oncoplot(maf = maf, top = 20, removeNonMutated = TRUE) titv = titv(maf = maf, plot = FALSE, useSyn = FALSE) #plot titv summary plotTiTv(res = titv)
Can you guide me how to change this code to be used for hg19?
I am looking forward to your comments