[BioC] AnnBuilder bug // R-2.0.0 // getList4GO

[John Zhang]

Thanks. I will have a look at the code and fix the problem.

>From: "Harry Athanassiou" <hathanassiou at automatedcell.com>
>To: <bioconductor at stat.math.ethz.ch>
>Date: Tue, 9 Nov 2004 01:22:42 -0500
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>Subject: [BioC] AnnBuilder bug // R-2.0.0 // getList4GO 
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>I'm trying to use AnnBuilder to make some custom annotation files for a
>non-standard microarray chip. In running the tests with R-2.0.0, I run
>acroos a problem in the function getList4GO. I'm not sure if this issue is
>due to R-2.0.0 or not.
> 
>Here's the issue:
>when the sub-function procOne is called by sapply, the names(goids) is NULL.
>Thus when procOne calls :
>    apply(temp, 1, vect2List, vectNames = c("GOID", "Evidence", "Ontology"))
>the number of list-elements to be named is mismatched.
> 
>I do not know how to make sapply pass the names() of its first argument to
>the FUN() it calls, so I modified procOne->procOne.new to drop the column
>"Evidence".
>And add this column with a trick afterwards.
> 
>I'm sure this is not the best solution, just worked for me
> 
>>>>
>getList4GO <- function (goNCat, goNEvi) 
>{
>    procOne <- function(goids) {
>        if (is.null(goids) || is.na(goids)) {
>            return(NA)
>        }
>        else {
>            temp <- cbind(goids, names(goids), goNCat[goids])
>            rownames(temp) <- goids
>            return(apply(temp, 1, vect2List, vectNames = c("GOID",
>"Evidence", "Ontology")))
>        }
>    }
>    
>    # the names(goids) do not get propagated through the sapply() in
>R-2.0.0!
>    # remove the column evidence
>    procOne.new <- function(goids) {
>        if (is.null(goids) || is.na(goids)) {
>            return(NA)
>        }
>        else {
>            temp <- cbind(goids, goNCat[goids])
>            rownames(temp) <- goids
>            return(apply(temp, 1, vect2List, vectNames = c("GOID",
>"Ontology")))
>        }
>    }    
>        
>    temp <- sapply(goNEvi, procOne.new)
>    names(temp) <- 1:length(temp)
>    
>    # add the evidence list-element
>    # do not know a better way will do a loop on an index to acc two arrays
>at the same time
>    for (r in 1:length(goNEvi)) {
>     if (!is.na(temp[r])) {
>      temp[[r]] <- c(temp[[r]], "Evidence"=names(goNEvi)[r])
>     }
>    }
>    
>    return(temp)
>}
>>>>
> 
>Harry Athanassiou
>BioInformatics manager
>Automated Cell, Inc
>
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Jianhua Zhang
Department of Biostatistics
Dana-Farber Cancer Institute
44 Binney Street
Boston, MA 02115-6084