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PoisonAlien / maftools

Summarize, Analyze and Visualize MAF files from TCGA or in-house studies.
http://bioconductor.org/packages/release/bioc/html/maftools.html
MIT License
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somaticInteractions function error #178

Closed mureal-bioinfo closed 3 years ago

mureal-bioinfo commented 5 years ago

Hello,

Although somaticInteractions() function works well for tutorial MAF data(tcga_laml.maf.gz), this function doesn't work for my MAF data. But, Most functions in maftools work well for my MAF data.

When I used somaticInteractions() function, I got these error messages below.

Error in sigPairs[i, ] : subscript out of bounds Calls: somaticInteractions -> -> lapply -> FUN Execution halted

Why did this happen? Could you please give me a solution?

A portion of my MAF data is as follows.

head(myMAF, n=3) Tumor_Sample_Barcode Hugo_Symbol Chromosome Start_Position End_Position 1 Sample-1 SAMD11 1 861369 861369 2 Sample-1 SAMD11 1 865694 865694 3 Sample-1 SAMD11 1 871334 871334 Reference_Allele Tumor_Seq_Allele2 Variant_Classification Variant_Type 1 G - Frame_Shift_Del DEL 2 C T Missense_Mutation SNP 3 G T Intron SNP

I downloaded maftools from github.
There are maftools version and R sessionInfo below.

Thank you!

packageVersion("maftools") [1] ‘1.7.5’

sessionInfo() R version 3.4.3 (2017-11-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.9 (Final)

Matrix products: default BLAS: ~/anaconda2/lib/R/lib/libRblas.so LAPACK: ~/anaconda2/lib/R/lib/libRlapack.so

locale: [1] LC_CTYPE=ko_KR.UTF-8 LC_NUMERIC=C
[3] LC_TIME=ko_KR.UTF-8 LC_COLLATE=ko_KR.UTF-8
[5] LC_MONETARY=ko_KR.UTF-8 LC_MESSAGES=ko_KR.UTF-8
[7] LC_PAPER=ko_KR.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=ko_KR.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

other attached packages: [1] RevoUtils_10.0.8 RevoUtilsMath_10.0.1

loaded via a namespace (and not attached): [1] compiler_3.4.3

PoisonAlien commented 5 years ago

Hi, How many samples do you have ?

mureal-bioinfo commented 5 years ago

Hi, thank you for your reply!

I tried using small samples less than three samples or large samples like about 100 or 300 samples. But, regardless of sample size, It didn't work... :(

Each sample has about 50000 variants.

However, when I used just 2000 variants in two samples, It didn't work.

I hope to solve this problem! thank you.

ShixiangWang commented 5 years ago

@QANGFQ Maybe you could provide small samples to PoisonAlien so he can debug this error. You can drag zip file into comment box.

PoisonAlien commented 5 years ago

It would be helpful if you could share your file. If its not possible, please give me some time I will get back yo you soon.

mureal-bioinfo commented 5 years ago

Because this data is private, I think that sharing data through e-mail would be better.
Could you let me know your e-mail address?

PoisonAlien commented 5 years ago

Hi, I understand. You can send me to anandmt3@gmail.com - also if its of concern, you could remove any personal data or change sample names.