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

[Harry Athanassiou]

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