Non standard Ti/Tv class: 1814TRUE
Closed this issue · 5 comments
Describe the issue
Hi, I am very new to maftools. I've been encountering an issue when running plotmafsummary and titv functions. The issue has been raised before and seems to be due to incorrect annotations of INDELS to SNPS. However, I generated my data using VEP and not annovar, therefore I'm not sure if the previous solution discussed for this warning could be applied here.
Please let me know if you need any further details. Any assistance will be greatly appreciated.
Command
Please post your commands and the output (errors or any unexpected output)
plotmafSummary(maf = maf_analysis, rmOutlier = TRUE, addStat = 'median', dashboard = TRUE, titvRaw = TRUE)
Warning message:
In titv(maf = maf, useSyn = TRUE, plot = FALSE) :
Non standard Ti/Tv class: 1814TRUE
maf.titv = titv(maf = maf_analysis, plot = FALSE, useSyn = TRUE)
Warning message:
In titv(maf = maf_analysis, plot = FALSE, useSyn = TRUE) :
Non standard Ti/Tv class: 1814TRUESession info
Run sessionInfo() and post the output below
R version 4.3.0 (2023-04-21)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.3.1
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Dublin
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] maftools_2.16.0
loaded via a namespace (and not attached):
[1] compiler_4.3.0 Matrix_1.6-1 DNAcopy_1.74.1 tools_4.3.0 RColorBrewer_1.1-3
[6] survival_3.5-7 rstudioapi_0.15.0 splines_4.3.0 grid_4.3.0 data.table_1.14.8
[11] lattice_0.21-8 Hi,
Thanks for the issue and sorry for the tardy response.
Would it be possible to share a reproducible example?
Thanks for getting back to me. Yes, all data is already fully anonymised so I don't mind sharing. Could you give me an email address to send this?
Hi,
This is my mail: anandmt3@gmail.com
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