parents vs ancestors

[christianholland]

Hi,
what exactly is the difference between the functions parents() and ancestors(). From my feeling parents should provide the direct upstream node while ancestors list all related upstream nodes. However, regarding my analysis parents and ancestors behave equally.

ontology = Ontology("doid")
anc = ancestors(term(ontology , "DOID:3458"))
par = parents(term(ontology , "DOID:3458"))
identical(anc, par) # TRUE

Is this intended?
Thanks in advance,
Christian

[lgatto]

Your expectation is correct. Thank you for reporting this issue, I'll look into it.

[lgatto]

Thanks again for reporting the bug. It is now fixed

> library(rols)

This is 'rols' version 2.9.1 

> ontology <- Ontology("doid")
> parents(term(ontology , "DOID:3458"))
Object of class 'Terms' with 1 entries
 From the DOID ontology
DOID:3459 
> ancestors(term(ontology , "DOID:3458"))
Object of class 'Terms' with 11 entries
 From the DOID ontology
  DOID:3459, DOID:1612 ... DOID:162, DOID:14566 

The fix is available on github immediately and should also become available on Bioconductor devel (2.9.1) and release (2.8.1).