gravatar for nazaninhoseinkhan

4 hours ago by

Iran, Islamic Republic Of

Dear all,

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

Nazanin



Source link