add symbol convesion for drosophila gene ID about tidybulk HOT 4 CLOSED

heya, I don't think it's essential to add it to tidybulk as people could do something like this

counts_annot <- mutate(counts_tt, symbol = mapIds(org.Dm.eg.db, keys=feature, keytype = "FLYBASE", column="SYMBOL", multiVals = "first"))

from tidybulk.

heya, I don't think it's essential to add it to tidybulk as people could do something like this

counts_annot <- mutate(counts_tt, symbol = mapIds(org.Dm.eg.db, keys=feature, keytype = "FLYBASE", column="SYMBOL", multiVals = "first"))

So you think we should drop ensembl_to_symbol function?

from tidybulk.

maybe, I don't have a strong feeling to drop it as I understand ensembl_to_symbol might be convenient for people who work with human and mouse but disadvantages are:

• unclear what annotation is being used, underlying annotation db, version etc (if using mapIds from the org.db package you've loaded to use, then you know)
• ensembl_to_symbol only works for human and mouse, you could make it work for drosophila but people with other species would need an alternative option
• extra maintenance to keep the annotation up to date for all species included in tidybulk, and also to document how the annotation is obtained and used in the tidybulk ensembl_to_symbol

if annotation can be done in a line or 2 like above with external packages, then maybe better to just do that & instead focus on documenting how people can get the annotation they need from the external packages?

from tidybulk.

Yes mostly agree, I can put the function as questioning life cycle. It would be nice to put the alternative example in the vignette/README so to remember it.

from tidybulk.