Can we apply CNest to SNP array CNV analysis? Also, we would like to inquire about the error encountered during the third step.

Dear Professor Tomas William Fitzgerald,

We are using your CNest package and have encountered some issues while applying it to SNP array CNV analysis. We truly appreciate your contributions and hope you can assist us in resolving these problems. If we successfully utilize your package, we will certainly cite your relevant work in our paper.

Our research involves using Affymetrix chips for CNV exploration, and we are employing the original APT tool for CNV analysis. We aim to apply your CNest package to these SNP array data to obtain more comprehensive and in-depth CNV results. Can you give me some advice? Do you suggest that your package can be used ?

While working with the example data provided in your package, we encountered the following error during the execution of the third step:

[ 07/28/2023 09:43:02 | INFO: Starting step3 07/28/2023 09:43:04 | ERROR: #Rscript /resources/run.R classify_gender test_proj_WES/bin test_proj_WES/index_tab.txt test_proj_WES/gender_qc.txt test_proj_WES/gender_classification.txt# failed with exit code 1. Loading required package: ViteRbi Loading required package: mixtools mixtools package, version 1.2.0, Released 2020-02-05 This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.

Error in sample.int(m, k) : cannot take a sample larger than the population when 'replace = FALSE' Calls: assign_gender -> kmeans -> sample.int ]

We suspect that this may be an issue related to R programming. However, as our expertise in the CNest package and R language is limited, we kindly request your assistance in debugging and identifying the root cause of this problem.

Your expert guidance is of great importance to the progress of our research, and we are eagerly looking forward to your help and support.

Thank you very much for your valuable time and assistance!

Sincerely,

Hi @orangeliu721001

I have also facing the similar error in the Step3. The command that I have used: index_tab=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/index_tab.txt bin_dir=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/bin qc_file=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_qc.txt ender_file=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_classification.txt cov_file=/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/mean_coverage.txt docker run -v "/media/ngslinux/External Disk/CNest_aug23/CNest-master/output:/output" -w "/output" -it --rm tomas81/cnest:dev step3 --indextab "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/index_tab.txt" --bindir "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/bin" --qc "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_qc.txt" --gender "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_classification.txt" --cov "/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/mean_coverage.txt"

The error that I'm facing: 08/08/2023 05:48:32 | INFO: Starting step3 08/08/2023 05:48:33 | ERROR: #Rscript /resources/run.R classify_gender /media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/bin /media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/index_tab.txt /media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_qc.txt /media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/gender_classification.txt# failed with exit code 1. Loading required package: ViteRbi Loading required package: mixtools mixtools package, version 1.2.0, Released 2020-02-05 This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.

Error in file(file, "rt") : cannot open the connection Calls: classify_gender -> read.table -> file In addition: Warning message: In file(file, "rt") : cannot open file '/media/ngslinux/External\ Disk/CNest_aug23/CNest-master/Ramadhar_CNEST/index_tab.txt': No such file or directory Execution halted

Did you manage to fix it? Thanks!

sorry for not getting back to you sooner - i have been on holiday.

This error looks like due to a low number of samples within the reference set - we have easily remove this but i am curious which test data set are you using?

Also for question on if CNest can be used with SNP array data.... it has not been designed for that but it could be possible, happy to have a chat / video call at somepoint if useful to go through what data you have and how to get CNest running nicely for you - just let me know if useful

Thank you for your kind response.

I am using the example data "CNest/nf/testdata/cram/" that you have provided on GitHub.

My SNP array utilizes the Affymetrix Axiom chip, and I have employed their Analysis Power Tools to obtain CNV data. Initially, my intention was to utilize your sample data to generate preliminary results. Ultimately, I aim to apply this process to SNP data. I appreciate your willingness to assist us in reviewing the data. I will first discuss this with my supervisor.

Best regards,

Ting-Yuan Liu

Tomas Fitzgerald @.***> 於 2023年8月13日週日下午5:13寫道：

sorry for not getting back to you sooner - i have been on holiday.

This error looks like due to a low number of samples within the reference set - we have easily remove this but i am curious which test data set are you using?

Also for question on if CNest can be used with SNP array data.... it has not been designed for that but it could be possible, happy to have a chat / video call at somepoint if useful to go through what data you have and how to get CNest running nicely for you - just let me know if useful

— Reply to this email directly, view it on GitHub https://github.com/tf2/CNest/issues/18#issuecomment-1676291701, or unsubscribe https://github.com/notifications/unsubscribe-auth/BBQQ7EVM52QD6ELSRZZRILLXVCLDRANCNFSM6AAAAAA23KJ4DM . You are receiving this because you were mentioned.Message ID: @.***>

-- 中國醫藥大學附設醫院-百萬人精準醫療計畫 助理研究員劉鼎元 04-22052121#12009 China Medical University Hospital, Taiwan Million-person precision medicine initiative, Department of Medical Research Assistant Researcher Ting-Yuan Liu

tf2 / CNest

Can we apply CNest to SNP array CNV analysis? Also, we would like to inquire about the error encountered during the third step. #18