Jeff Gentry wrote:
> Hi there ...
>
> I was looking to work with some of the Bioconductor annotation packages
> directly in Python and came across Rpy2.
Good to see Bioconductor veterans here ! ;-)
Rpy2 should/will do more with BioC (but more some time later).
> The first problem is just one of
> inexperience, I'm probably doing things all wrong and that could be the
> source of my issue :) I did just notice something odd:
>
> t = robjects.r('get("1000_at", hgu95av2SYMBOL)')
>>>> t
> <RVector - Python:0x2aaab0e9ca70 / R:0x233c208>
>>>> t[0]
> 'MAPK3'
>
> So far so good.
>
> t = robjects.r('get("1017_at", hgu95av2SYMBOL)')
> ## note that in R, this returns NA
>>>> t
> <RVector - Python:0x2aaab0e9cb90 / R:0x207dfc8>
>>>> t[0]
> True
>
>
> Is this expected behavior (True replacing NA)?
>
Definitely not. This is a bug.
I am also getting:
>>> robjects.r('NA')[0]
True
> Also, while I'm here, is there a way to skip the intermediate step, ie
> have the singular Python object returned instead of an RVector?
Two things:
1) To a large extent, there is no scalar value in R, only length-one
vectors.
For example, in R:
> length(NA)
[1] 1
2) The RVector is actually a rabbit-hole leading to the R world. The
values are only copied / becoming Python objects when accessed through
the '[' operator.
For automagic subsetting of length-one vectors, you can try tweaking the
robjects-level converter like shown here:
http://rpy.sourceforge.net/rpy2/doc/html/robjects_convert.html#a-simple-example
Thanks for the bug report,
L.
> Thanks
> -J
>
>
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