Problem with knitr package

[SwagatikaSahoo2023]

Dear COSMOSR Authors,
I am currently running the tutorial.Rmd in R Studio.
I am getting the below error while running the chunk for preparing the inputs.

"Error in preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network, :
could not find function "preprocess_COSMOS_metabolism_to_signaling"

Please advise further.
Best
Swagatika Sahoo

[adugourd]

Hi,

thanks for your interest in running our tool :)

It's difficult to be sure what's going on with this limitted information, but it appears that the cosmos library is not loaded properlly if you get this error.

If you want a more detailled tutorial, you can also have a look here: https://github.com/saezlab/NCI60_cosmos

Cheers,

Aurelien

[SwagatikaSahoo2023]

Dear Aurelien Thanks for your prompt reply. I installed the codes from the github page, as mentioned in the tutorial https://embl-ebi.cloud.panopto.eu/Panopto/Pages/Viewer.aspx?id=318f7091-b6bf-44ee-939f-adb10121fc1b Furthermore, I have also downloaded codes from NCI60_cosmos & saezlab/decoupleR github pages. I am following the steps as mentioned in the tutorial, and it continues to complain as, "Error in preprocess_COSMOS_metabolism_to_signaling(meta_network = toy_network, : could not find function "preprocess_COSMOS_metabolism_to_signaling"" Please let me know if I am missing something. P.S. I am running from tutorial.Rmd in the vignettes folder. Best Swagatika Sahoo

…

On Mon, May 8, 2023 at 5:13 PM Aurelien Dugourd ***@***.***> wrote: Hi, thanks for your interest in running our tool :) It's difficult to be sure what's going on with this limitted information, but it appears that the cosmos library is not loaded properlly if you get this error. If you want a more detailled tutorial, you can also have a look here: https://github.com/saezlab/NCI60_cosmos Cheers, Aurelien — Reply to this email directly, view it on GitHub <#28 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/A7T6TE7UXYJAQYH56OKKN23XFDL5FANCNFSM6AAAAAAXZX3RII> . You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Swagatika Sahoo, Ph.D. R&D Senior Scientist Vantage Research Pvt Ltd 2 Sivasamy Street, Mylapore Chennai 600004, Tamil Nadu www.vantage-research.net Alternate Email: ***@***.*** Skype: swagatika05 https://in.linkedin.com/in/dr-swagatika-sahoo-ph-d-ab520723 --- This message is confidential and may contain privileged information. It is intended for the named recipient only. If you receive it in error please notify me and permanently delete the original message and any copies.

[gabora]

When you call
library(cosmosR)
do you get any error?