maftool package: No non-synonymous mutations found Check `vc_nonSyn`` argumet in `read.maf` for details

[celluq]

I have download the SNV data from TCGA database. But this error was reported when a maf file was read by read.maf command. So what's the meaning of that? How to fix it? Thank you so much for your help.

[ShixiangWang]

This typically means the input MAF data does not contain mutations that may have effects (on gene function). If you want to include all mutations, you should reset the vc_nonSyn option.

[celluq]

Thank you so much for your help!

[zyffzi]

Could I know how to reset the vc_nonSyn option? Thanks a lot.

[ShixiangWang]

@zyffzi Run ?read.maf in R console. Change the option to what you want to analyze.

[zyffzi]

Thank you very much! I find that I can often successfully read individual MAT files.

However, when I use the Apply function to read all the MAT files in the folder: It displayed the same warning in the end:

Have you ever encountered such a situation before? How can I solve it？ Thank you so much for your help.

[ShixiangWang]

For tcga data, you can use TCGAbiolinks. A solution for your error is manually set the vc_nonSyn to all mutation types in the read.maf.

[Yizhou-Y]

Could you tell me how to set the vc_nonSyn to all mutation types？By vc_nonSyn = all/ture？

[ShixiangWang]

library(maftools)

laml.maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools") #MAF file
laml.clin = system.file('extdata', 'tcga_laml_annot.tsv', package = 'maftools') #clinical data
laml = read.maf(maf = laml.maf, clinicalData = laml.clin, vc_nonSyn = c("Frame_Shift_Del", "Frame_Shift_Ins" ))

[matteocostacurta]

Hi, I am encountering exactly the same problem (described at the top).

I am testing maftools for use with 1000+ samples downloaded from TCGA. I am importing them manually and treating them as they were non-TCGA files as I will be obtaining mafs from whole exome sequencing of a bunch of clinical samples.

This is my code:

library(maftools)

setwd("/my/directory/path/with/maf/files")

file_list <- as.list(list.files(pattern="*.maf"))
maf_list <- list()

for (i in file_list) {
  print(i)
  maf_list[[i]] <- read.maf(maf=`i`, vc_nonSyn = NULL)
}

The for loop for read.maf stops at sample number 114 of 1091 with the aforementioned error.

I have tried to replace vs_nonSyn = NULL with any and all of the options in the description of the parameter vs_nonSyn in ?read.maf. When I do that, it stops at either sample number 1, or at sample 114 again.

Could you please advice how to solve the issue?

Thank you so much!

[ShixiangWang]

Why not bind all maf files first and then import it with maftools?

library(data.table)
library(maftools)

file_list <- list.files(pattern="*.maf")
maf_list = lapply(file_list, function(x) data.table::fread(x))
maf = rbindlist(maf_list)
mafObj = read.maf(maf)

[matteocostacurta]

It works a treat, thank you!

Why not bind all maf files first and then import it with maftools?

library(data.table)
library(maftools)

file_list <- list.files(pattern="*.maf")
maf_list = lapply(file_list, function(x) data.table::fread(x))
maf = rbindlist(maf_list)
mafObj = read.maf(maf)

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