Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

No non-synonymous mutations found #1058

Open
aeozdemr opened this issue Oct 16, 2024 · 1 comment
Open

No non-synonymous mutations found #1058

aeozdemr opened this issue Oct 16, 2024 · 1 comment

Comments

@aeozdemr
Copy link

Hi first of all thanks for this great tool!

I am trying to read my .maf file but I want classify all the mutations as non-silent because I need all for oncoplot and I want to see the mutations if they are even silent.

For this I tried to use "nonSyn = c("Frame_Shift_Del", "Frame_Shift_Ins", "Splice_Site",
"Translation_Start_Site","Nonsense_Mutation", "Nonstop_Mutation", "In_Frame_Del","In_Frame_Ins", "Missense_Mutation","intergenic")" for nonSyn option, however even though there are mutations in my .maf file it still says no non-synonymous mutations found. How can I skip the part where read.maf checks for non-synonymous mutations or how can I classify all mutations as nonSyn.

Thanks.

@PoisonAlien
Copy link
Owner

Hi,

Are you sure the values in Variant_Classification column match those provided in nonSyn?

If you'd like to consider all types as nonSyn, please try as below

> laml.maf = system.file("extdata", "tcga_laml.maf.gz", package = "maftools") #MAF file
> m = data.table::fread(input = laml.maf)
> all_vcs = m[,.N,Variant_Classification][,Variant_Classification]
> print(all_vcs)
 [1] "Splice_Site"       "Missense_Mutation" "Silent"            "Frame_Shift_Del"   "Nonsense_Mutation" "Intron"            "Frame_Shift_Ins"   "RNA"               "In_Frame_Del"     
[10] "IGR"               "In_Frame_Ins"      "5'Flank"   
> m = maftools::read.maf(maf = m, vc_nonSyn = all_vcs)

I hope this helps.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants