isoAnnotate error

[zxl124]

Thank you so much for this useful package.

When running isoAnnotate I encountered the following error:

Error in `[[<-.data.frame`(`*tmp*`, "edit_mature_position", value = c("NA",  : 
  replacement has 3762 rows, data has 3504

The input was generated using mirtop export, then loaded into isomiRs using IsomirDataSeqFromMirtop. Other isomiRs functions seemed to work correctly. Not sure if this error originated from mirtop or isomiRs.

isomiRs version 1.16.2 was installed using Bioconductor on R 4.0.2.

Thanks in advance for looking into this.

[lpantano]

Sorry I missed this, there was an issues with my github notification and I missed a bunch. Happy to help if still needed.

[bounlu]

I get the same error.

> isoAnnotate(ids_counts)
Error in `[[<-.data.frame`(`*tmp*`, "edit_mature_position", value = c("NA",  : 
  replacement has 2645 rows, data has 2396

[lpantano]

Do you think you can share the R object for me to take a look? And what version of R are you using? Thanks

[bounlu]

Unfortunately I am not able to share the R object but I think it is a reproducible error as other users also experienced it. I am using R 4.3.2.

[karlaarz]

Hello, I was wondering if you were able to solve this? I get the same error:

Error in `[[<-.data.frame`(`*tmp*`, "edit_mature_position", value = c("NA",  : 
  replacement has 966 rows, data has 887

I'm using R.4.2.0

[lpantano]

Hi, I couldn't find the error, do you think you can find some data to share? it would be much easier to find the problem. I could be some small dataset, maybe only a couple of samples or anonymized the samples names. Happy to help if I have something to work with.

Thanks

[karlaarz]

Of course! Is there an email I can send you the data to?

[lpantano]

you can use the email in my GitHub profile. thanks!

[karlaarz]

Great! I have sent it now (:

[lpantano]

I pushed a change, if you could install from the main branch to try again.

But I think the issue is from mirtop as mention here: miRTop/mirtop#80

I think I need to try to reproduce that error. Any change I can get the data from the mirtop export step? Maybe only having WT1 and WT2 samples are enough.

[lpantano]

just pinging here, in case you can share those files.thanks

[karlaarz]

Hi Lorena, sorry for my late reply. I had the chance to run the pipeline again using the latest version of R (4.4.1), and the latest installation from the main branch that you suggested, and now I don't get the error anymore. Maybe the error was because my previous version of R was 4.1? Thanks for the help!

[lpantano]

it could be, but I pushed a fixed to main branch and to the dev in bioconductor so maybe that helped as well.