Issue with mutation signature extraction and I need a help

[eunksung]

Hello,
I tried both Sigminer (version 2.2.0) and Sigflow (version 2.1) to extract mutation signatures, but it kept getting errors while it was running the extracting part. This is the error message from Sigminer with R: Error in x[, sort(colnames(x))] : incorrect number of dimensions. This is the error message from Sigflow: An error is detected in extract process. Quit the program! error in evaluating the argument 'x' in selecting a method for function 't': 'x' must be an array of at least two dimensions

I used only MAF for both Sigminer and MAF and VCF for Sigflow. I generated these VCFs from BAM files that I downloaded from EGA, and used VCF2MAF to generate MAFs. Also, I ran the Sigminer and Sigflow with three different. They all gave the same error message.

When I tested Sigflow with test files in sigflow/test, it generated all files listed in the manual.
This is the command that I used for Sigflow:
sigflow extract -i /Users/eunsung/Desktop/Project/MAF/LU-14.snvs.vep.maf -o /Users/eunsung/Desktop/Project/Sigflow_results/LU-14_maf -m MAF -r 10 -T 4 --max 10 -v

It created SBS-6, 96, and 1536 matrix, and created DBS-78 and 1248 matrix. After the message "Outputing tally results for SBS", the program stopped with the message I mentioned above.

For Sigminer, I used this code:
mt_tally2 <- sig_tally(
LU_FF55,
method = "S",
ref_genome = "BSgenome.Hsapiens.1000genomes.hs37d5",
mode= c("SBS"),
genome_build = "hg38",
use_syn = TRUE, add_trans_bias = TRUE
)

And this is the result from it:
ℹ [2023-05-10 22:21:50]: Creating SBS sample-by-component matrices.
✔ [2023-05-10 22:21:50]: SBS-6 matrix created.
✔ [2023-05-10 22:21:50]: SBS-96 matrix created.
✔ [2023-05-10 22:21:50]: SBS-1536 matrix created.
✔ [2023-05-10 22:21:53]: SBS-24 (6x4) matrix created.
✔ [2023-05-10 22:21:55]: SBS-384 (96x4) matrix created.
✔ [2023-05-10 22:21:57]: SBS-6144 (1536x4) matrix created.
ℹ [2023-05-10 22:21:57]: Return SBS-192 as major matrix.
Error in x[, sort(colnames(x))] : incorrect number of dimensions

When I check the MAFs, all required inputs were there in the same format as in the test except Turmor_Sample_Barcode. All of variables of the field were Tumor in my MAFs.

Please, let me know if there are any other information you are required.

Thank you.

[ShixiangWang]

@eunksung Thanks for your question. Could you share your data LU_FF55 or part of it to shixiang1994wang@gmail for debugging purposes?

[eunksung]

Hello, Thank you for reaching out to me, Dr. Wang. Because of the file size, I sent you a Google drive link to share. If it does not work, please, let me know. Once again thank you for your concern. LU-FF55.snvs.vep.maf <https://drive.google.com/file/d/17_CdFp8Q7_ge8-YfO6ec1LZ7QHdNDEsf/view?usp=drive_web>

…

On Mon, May 15, 2023 at 2:14 AM Shixiang Wang (王诗翔) < ***@***.***> wrote: @eunksung <https://urldefense.com/v3/__https://github.com/eunksung__;!!LIr3w8kk_Xxm!p3pe4kayKV3C1t4-x-MlK2nEejGcbrthjYobiEEugZxrY9-bU1PjWilsrr0d57d81BiWSiom-BijzUCzLOMkJFM$> Thanks for your question. Could you share your data LU_FF55 or part of it to ***@***.*** for debugging purposes? — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/ShixiangWang/sigminer/discussions/432*discussioncomment-5903055__;Iw!!LIr3w8kk_Xxm!p3pe4kayKV3C1t4-x-MlK2nEejGcbrthjYobiEEugZxrY9-bU1PjWilsrr0d57d81BiWSiom-BijzUCzAFaBg5o$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A27HBIL76DDIYVVGSLSTEXTXGHXWZANCNFSM6AAAAAAX7BVFKM__;!!LIr3w8kk_Xxm!p3pe4kayKV3C1t4-x-MlK2nEejGcbrthjYobiEEugZxrY9-bU1PjWilsrr0d57d81BiWSiom-BijzUCz5c8NIsU$> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ShixiangWang]

After I click the link, I got a message that I have no right to access.

[ShixiangWang]

@eunksung The package is typically handling multiple samples. However, you have only one sample and the data caused some unexpected class changes from "matrix" to "vector". Thanks for your reporting for making sigminer more robust. I have updated the package, could you install and re-run it?

devtools::install_github("ShixiangWang/sigminer")

library(sigminer)

LU_FF55 = read_maf("~/../Downloads/LU-FF55.snvs.vep.maf")

mt_tally2 <- sig_tally(
  LU_FF55,
  method = "S",
  mode= c("SBS"),
  genome_build = "hg19",
  use_syn = TRUE, 
  add_trans_bias = TRUE
)

# ref_genome = "BSgenome.Hsapiens.1000genomes.hs37d5",

LU_FF55@data$Tumor_Sample_Barcode

BTW. Your data is a little strange to me, there are too many silent mutations in your data just for one sample.

[eunksung]

Thank you once again for your help. As you mentioned, I tried to find the mutation signature of each sample. I will try to use both single and combined samples after re-install the sigminer. If there is still an issue, then I will let you know. I hope you have a great day. Thank you. Kind regards, Eun Kyu Sung

…

On Tue, May 16, 2023 at 7:18 PM Shixiang Wang (王诗翔) < ***@***.***> wrote: @eunksung <https://urldefense.com/v3/__https://github.com/eunksung__;!!LIr3w8kk_Xxm!r1_A71Lfa3byzFEVm1bZdEmEIKpsnEWGflzO1QqkErJ-dZNYDYTxcZTykzbR1bGjUYU88dXNRa3zEKVLR--7HUY$> The package is typically handling multiple samples. However, you have only one sample and the data caused some unexpected class changes from "matrix" to "vector". Thanks for your reporting for making sigminer more robust. I have updated the package, could you install and re-run it? devtools::install_github("ShixiangWang/sigminer") library(sigminer) LU_FF55 = read_maf("~/../Downloads/LU-FF55.snvs.vep.maf") mt_tally2 <- sig_tally( LU_FF55, method = "S", mode= c("SBS"), genome_build = "hg19", use_syn = TRUE, add_trans_bias = TRUE ) # ref_genome = "BSgenome.Hsapiens.1000genomes.hs37d5", ***@***.***$Tumor_Sample_Barcode BTW. Your data is a little strange to me, there are too many silent mutations in your data just for one sample. — Reply to this email directly, view it on GitHub <https://urldefense.com/v3/__https://github.com/ShixiangWang/sigminer/discussions/432*discussioncomment-5922454__;Iw!!LIr3w8kk_Xxm!r1_A71Lfa3byzFEVm1bZdEmEIKpsnEWGflzO1QqkErJ-dZNYDYTxcZTykzbR1bGjUYU88dXNRa3zEKVL5j0XxVo$>, or unsubscribe <https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/A27HBIKDPADR6C2NLBCD2K3XGQYQZANCNFSM6AAAAAAX7BVFKM__;!!LIr3w8kk_Xxm!r1_A71Lfa3byzFEVm1bZdEmEIKpsnEWGflzO1QqkErJ-dZNYDYTxcZTykzbR1bGjUYU88dXNRa3zEKVL_93zSyw$> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[ShixiangWang]

Ok. If you have further question, please open another issue :).