pandaR function is missing from the netZooR code for R functionality not using python integration

[jordanwhitlock]

Was looking to use lioness with panda from the netZooR package. Saw that there was a recent update 18 days ago to this github repository. When looking through the netZooR source code at https://rdrr.io/github/netZoo/netZooR/api/ , I noticed that the pandaR function is no longer listed, only panda.py

Furthermore, when trying to implement panda within lioness using R studio without the reticulate integration to run python through R, the lioness example listed here: https://rdrr.io/github/QuackenbushLab/pandaR/man/lioness.html is not functional, I believe becasue it is trying to call on the panda function within netZooR, which is no longer present. As a result the following error is presented while trying to generate the regulatory network within panda:

Error in tfCoopNetwork[Idx] <- ppi[, 3] : NAs are not allowed in subscripted assignments

I have run into this error previously running panda on its own, and it was being caused by “Idx <- (Idx2-1)*num.TFs+Idx1” in the TFnetwork generating code of the panda function. It’s is because the previous 2 lines with match don’t work as the code author things they do, they introduce NAs. This was priorly addressed by an update to the netZooR package. Any assitance on this would be greatly appreciated!

[marouenbg]

Hi @jordanwhitlock ,
Thanks for using netZoo, we've been updating the package recently and I am waiting for the final tests to run. I will reach out to you later today for a fix to this bug.
Marouen

[jordanwhitlock]

Thank you so much! ~Jordan Jordan H. (Barham) Whitlock | University of Alabama at Birmingham Graduate Biomedical Sciences | Genetics, Genomics, and Bioinformatics The Lasseigne Lab | Graduate Trainee | #BecauseScience

…

________________________________ From: Marouen ***@***.***> Sent: Friday, October 29, 2021 10:55 AM To: netZoo/netZooR ***@***.***> Cc: Whitlock, Jordan H ***@***.***>; Mention ***@***.***> Subject: Re: [netZoo/netZooR] pandaR function is missing from the netZooR code for R functionality not using python integration (Issue #224) Hi @jordanwhitlock<https://github.com/jordanwhitlock> , Thanks for using netZoo, we've been updating the package recently and I am waiting for the final tests to run. I will reach out to you later today for a fix to this bug. Marouen — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#224 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AOZGLVJGSE3CWKML2P2EVP3UJK7VLANCNFSM5G5GSW4Q>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.

[marouenbg]

Hi @jordanwhitlock ,

This documentation website ( https://rdrr.io/github/netZoo/netZooR/api/ ) might take some time to update. We're maintaining our R package docs on https://netzoo.github.io/netZooR/.

panda() is a pure R function that is provided by the pandaR package, which means it is not exported by the netZooR package, however it is loaded at the same time with netZooR (library(netZooR)) because it is set as a dependency.

I just tried the lioness example in this vignette (https://rdrr.io/github/QuackenbushLab/pandaR/man/lioness.html ) and it worked for me on R4.1. Try installing netZooR again and see if ?panda works and let me know if you have any questions!

Marouen

[marouenbg]

HI @jordanwhitlock ,
Feel free to reopen the issue if your question has not been answered.
Marouen