create_tt_from_bam_sam_bulk function recuires org.Hs database and is therefore incompatible with other organisms

[richardstoeckl]

Hello and thank you for your great package!

I want to use this package with data from Arbabidopsis thaliana.
Sadly, when I try to use the "tidybulk_SAM_BAM()" wrapper function I get the error message
Error when evaluating the argument 'x' for the function 'mapIds': there is no package called ‘org.Hs.eg.db’
and after I install the "org.Hs.eg.db", I get the Error
Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENTREZID'. Please use the keys method to see a listing of valid arguments.

So I had a look at the sourcecode and if I understand it correctly, the function "create_tt_from_bam_sam_bulk()" calls the function "AnnotationDbi::mapIds()" when a external annotation file is specified (which is required since Arabidopsis is not provided with the subread package) with the hard-coded default parameter set to "org.Hs.eg.db", which is obviously not for every organism.

Is there a way to remove this dependency or make it customizable for other organisms?

Thanks,
Richard

[stemangiola]

Hello Richard.

Yes, indeed some functions are geared toward human because that's is what I mostly do. Surely can be made more generic.

In the next two weeks, I am quite overwhelmed. I can have a look after that.

Also if you want to have a go to edit the function yourself, and propose a change, this would be a great way to contribute. (That's always the hope with Github ;) ). Of course, that's entirely optional.

[stemangiola]

Hello @richardstoeckl, few weeks become many months (sorry about that).

Would you like to try again? The branch where I fixed it is

allow-mapping-to-other-genomes