search

spxuw / DKI

MIT License
34 stars 10 forks source link

How can we obtain the GCN.tsv file. #4

Open liaohu1231 opened 10 months ago

Axolotl233 commented 10 months ago

I have the same question there, whether i could use GCN file provided in data? If it is convenient for you, we can communicate by email. My address is axolotl233@gmail.com

PonderLi commented 10 months ago

Hi, I used the GCN file provided by demo GCN.csv to run Keystoneness_computing.R and I met an error: Error in as.numeric(q_i_null) %*% as.matrix(GCN_full) : non-conformable arguments

Could you give me some suggestions about how to make my own GCN.csv? THANKS!

spxuw commented 10 months ago

You can use Picrust2 ( https://github.com/picrust/picrust2/wiki/Full-pipeline-script) to predict the GCN (KO_predicted.tsv.gz generated by Picrust2) if the data is 16S.

On Sun, Dec 24, 2023 at 5:59 AM ponderLi @.***> wrote:

Hi, I used the GCN file provided by demo GCN.csv to run Keystoneness_computing.R and I met an error: Error in as.numeric(q_i_null) %*% as.matrix(GCN_full) : non-conformable arguments

Could you give me some suggestions about how to make my own GCN.csv? THANKS!

— Reply to this email directly, view it on GitHub https://github.com/spxuw/DKI/issues/4#issuecomment-1868489344, or unsubscribe https://github.com/notifications/unsubscribe-auth/AATVE3X6BA5X6HXUN4ZTDV3YLADJRAVCNFSM6AAAAABASZWUJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRYGQ4DSMZUGQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

PonderLi commented 10 months ago

You can use Picrust2 ( https://github.com/picrust/picrust2/wiki/Full-pipeline-script) to predict the GCN (KO_predicted.tsv.gz generated by Picrust2) if the data is 16S. … On Sun, Dec 24, 2023 at 5:59 AM ponderLi @.> wrote: Hi, I used the GCN file provided by demo GCN.csv to run Keystoneness_computing.R and I met an error: Error in as.numeric(q_i_null) %% as.matrix(GCN_full) : non-conformable arguments Could you give me some suggestions about how to make my own GCN.csv? THANKS! — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/AATVE3X6BA5X6HXUN4ZTDV3YLADJRAVCNFSM6AAAAABASZWUJGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRYGQ4DSMZUGQ . You are receiving this because you are subscribed to this thread.Message ID: **@.***>

Thank you for your prompt response! I sincerely appreciate your input. My data comprises metagenomic data, meaning that upon aligning them with KEGG or other functional databases, I obtain a table with genes as rows and samples as columns. I have a question to seek your guidance: Does this table consist solely of 0 and 1? Thank you for your time and assistance.