[BioC] [PATCH] Fix options in GSVA

[Robert Castelo]

hi again everybody,

the original post was not published at the list, so this is just to 
confirm that the fix that you kindly provide has been included in the 
updated development (1.7.5) and release (1.6.2) versions of the GSVA 
package.

thanks again for bug reporting, and this time, even fixing!! :)
robert.


On 01/16/2013 11:55 AM, Luca Beltrame wrote:
> Hello,
>
> While trying to debug the previous issue in GSVA I noticed that there is an
> error in one of the methods defined for the GSVA class.
>
> In particular, the signature expr="matrix", gset.idx.list="GeneSetCollection",
> annotation="character" is not handled correctly: the code calls
> Biobase::annotation and that causes an error ("closure" cannot be coerced to
> "character"). Since annotation for that signature is a character, I changed
> like in the attached patch, which fixes the problem for me.
>
> Would you be able to apply it to GSVA? Thanks in advance.
>


---gsva_fix_options.diff----------------------------------------------------

--- GSVA/R/gsva.R.orig	2013-01-16 11:51:40.874694759 +0100
+++ GSVA/R/gsva.R	2013-01-16 11:19:36.518699558 +0100
@@ -123,7 +123,7 @@
        cat("Mapping identifiers between gene sets and feature names\n")

      mapped.gset.idx.list <- GSEABase::mapIdentifiers(gset.idx.list,
- 
GSEABase::AnnoOrEntrezIdentifier(Biobase::annotation))
+ 
GSEABase::AnnoOrEntrezIdentifier(annotation))
    }

    ## map to the actual features for which expression data is available

-- 
Robert Castelo, PhD
Associate Professor
Dept. of Experimental and Health Sciences
Universitat Pompeu Fabra (UPF)
Barcelona Biomedical Research Park (PRBB)
Dr Aiguader 88
E-08003 Barcelona, Spain
telf: +34.933.160.514
fax: +34.933.160.550