Question about pathway data file while running PathGNN

[Haangik]

Hi @BioAI-kits.
Thank you for providing your PathGNN. I have a question while I am trying to use PathGNN with the data you provided.

Firstly, I have a trouble of running the Main function part of 'data.py' because the function 'generate_gmt' couldn't find a file named 'Pathway/pathways/R-HSA-5668914.txt', which may be likely to the file representing genes of the first pathway in 'dtail_file'.
I couldn't find that file from your repository so far, even there is no directory 'pathway' inside the 'Pathway' directory.
Do I need any additional steps for generating or downloading that file?
I would appreciate it if you could help me on this matter.

Moreover, I think it would be useful for everyone who interested to your valuable tool if you could provide intermediate files such as the SSGSEA result of the expression dataset or 'pathway_reactome_ssgsea.pt' of your LUAD demo protocol. Could you consider providing those files on this repository?

Best regards
Thank you.

[BioAI-kits]

Dear, Thanks for your interesting to our work ! You are right, those files, like 'Pathway/pathways/R-HSA-5668914.txt', include the pathway information, which we download from public database. Those files are very big size, so I couldn’t upload to Github. In the next week, I will upload those files to Google Driver and add comments to the code for better understanding. When I'm done, I'll sync the link to Github. Best regards Thank you. 发件人: Haangik 发送时间: 2023年2月7日 2:03 收件人: BioAI-kits/PathGNN 抄送: Billy; Mention 主题: [BioAI-kits/PathGNN] Question about pathway data file while runningPathGNN (Issue #1) Hi @BioAI-kits. Thank you for providing your PathGNN. I have a question while I am trying to use PathGNN with the data you provided. Firstly, I have a trouble of running the Main function part of 'data.py' because the function 'generate_gmt' couldn't find a file named 'Pathway/pathways/R-HSA-5668914.txt', which may be likely to the file representing genes of the first pathway in 'dtail_file'. I couldn't find that file from your repository so far, even there is no directory 'pathway' inside the 'Pathway' directory. Do I need any additional steps for generating or downloading that file? I would appreciate it if you could help me on this matter. Moreover, I think it would be useful for everyone who interested to your valuable tool if you could provide intermediate files such as the SSGSEA result of the expression dataset or 'pathway_reactome_ssgsea.pt' of your LUAD demo protocol. Could you consider providing those files on this repository? Best regards Thank you. — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you were mentioned.Message ID: ***@***.***>

[BioAI-kits]

Hi， I have upload pathways files. But you should unzip this file before using.