[BioC] PFAM family names

[Marc Carlson]

Daniel Gatti wrote:
> I'm trying to get text descriptions of PFAM family names from the PFAM 
> package.  I've tried to run the example code from the pfamAC2PDB help.
>
>  > AC2DE <- pfamAC2DE()
>  > head(AC2DE)
> $PF00244
> [1] "14-3-3 protein"
>
>  > pfamAC2DE(ac=sample(names(AC2DE), 3))
> Error in sample(names(AC2DE), 3) :
>    cannot take a sample larger than the population when 'replace = FALSE'
>  > length(AC2DE)
> [1] 1
>  > names(AC2DE)
> [1] "PF00244"
>
> It seems that the list contains only one value.  How do I get 
> descriptions for all of the PFAM families?
>
> Thanks,
> Dan Gatti
> UNC-CH
>
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>   

The original PFAM has apparently been broken for a while now, and this
was brought to my attention very recently.  So I have spent a lot of
time creating an entirely new PFAM package called PFAM.db.  The new
package also has the advantage of being a modern .db annotation
package.  This package is in the development branch of bioconductor
(2.2).  You can find it here:

http://www.bioconductor.org/packages/2.2/data/annotation/html/PFAM.db.html

Or you can just use biocLite to grab it from the devel version of R:
biocLite("PFAM.db")

Then you will want to look at the equivalent environment to what you
were looking at here. So for the old pfamAC2DE map the new name is now
just called PFAMDE.  This is just the new convention for naming used
across all of the new annotation packages.  So knowing that, you can do
something like this to get what you want:

library(PFAM.db)
AC2DE <- as.list(PFAMDE)

Please let me know if you have further questions.

Cheers,

    Marc