Entering edit mode
4.1 years ago
nazaninhoseinkhan
▴
530
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
Default in maftools is
hg19
unless you change thatOnly gisticChromPlot uses chromosome length information for plotting. Default is hg19 and can be changed with ref.build argument.
Hi, After running "
maf <- GDCquery_Maf("CESC", pipelines = "mutect") %>% read.maf"
, I get this :-
In line 2 you can see the version of genome reference is hg38
Actually you don't need this
I suggest you may just download maf file for cancer of your interest here
You then use
merge_maf
function from Maftools itself to read what you have downloaded (click on the mutation annotation ) the files name isgdac.broadinstitute.org_CESC.Mutation_Packager_Oncotated_Calls.Level_3.2016012800.0.0
Default in maftoools is
hg19