Error in sleuth_live using gene_mode=TRUE

[lmigueel]

Hello,

I got an error when I used the argument gene_mode=TRUE on sleuth_live. The first part of the figure shows a bug in gene box. When I tryed to find one gene, I got the error "Error: could not find function "gene_from_gene" (second part of the figure). How I can solve this? Anyone can help me?

Thanks.

[warrenmcg]

Hi @lmigueel, thanks for pointing this out! This was a function that was supposed to be present that got lost in the shuffle of merging branches, and we didn't catch it during testing. I'm doing an emergency patch now.

[warrenmcg]

Hi @lmigueel, the issue is fixed. If you reinstall sleuth using devtools, the newest master commit should be installed, with the method restored.

devtools::install_github('pachterlab/sleuth')

[lmigueel]

Hi @warrenmcg,

Thanks for your reply. I reinstalled sleuth but I got one different error. Look the figure.
It's seems that sleuth can not find the gene agregated column. The column ens_gene is on my transcript2gene file.

Regards,

[warrenmcg]

Hi @lmigueel, sorry you are continuing to have problems and thanks for bringing this back to our attention. I've identified the issue, and hopefully get a patch out soon.

[warrenmcg]

Hi @lmigueel, I've pushed a patch. If you want to immediately work with it before it gets folded into master, you can do so by doing the following:

devtools::github_install('warrenmcg/sleuth', ref = 'patch_g2g')

This is exactly the same version except with the patched included. Let me know if you experience any further difficulties. We'll close this issue when the patch gets folded into master

[lmigueel]

Hi @warrenmcg ,

I've tryed to plot again and still shows the same error "Error in eval: object 'ens_gene' not found".

I only installed from github, like you said, and start sleuth_live. Do you think that is necessary run all script again? I mean sleuth_prep and sleuth_fit again?!

Thanks.

[warrenmcg]

@lmigueel, did you use the exact line that I gave you? This patch is not on master yet, so doing the usual install_github will result in no change and the same error. My patch works on my end, so it should work on yours.

[lmigueel]

Hello @warrenmcg ,

I would like to thank you. The bug is fixed.

Regards,