[BioC] resolveMaps removed from AnnBuilder?

[James W. MacDonald]

Hi Ben,

Wittner, Ben, Ph.D. wrote:
> Did resolveMaps get removed from AnnBuilder?
> It still has a help entry, but the function does not appear to exist.
> I ask because I wrote code that uses the function.
>  

It's there, but is now sealed in the namespace:

 > resolveMaps
Error: object "resolveMaps" not found
 > AnnBuilder:::resolveMaps
function (maps, trusted, srcs, colNames = NULL, outName = "",
     asFile = TRUE)
{
     doOneRow <- function(vect) {
         temp <- vect[!is.null(vect)]
         temp <- temp[!is.na(temp)]
         temp <- temp[toupper(temp) != "NA"]
         if (length(temp) == 0) {
             vote <- c(NA, length(vect))
         }
         if (any(!is.na(temp[trusted]))) {
             vote <- getVote(temp[trusted])
         }
         else {
             if (any(!is.na(temp[srcs]))) {
                 vote <- getVote(temp[srcs])
             }
             else {
                 vote <- c(NA, length(c(trusted, srcs)))
             }
         }
         return(c(vect[setdiff(names(vect), c(trusted, srcs))],
             vote[1], vote[2]))
     }
     if (!is.null(colNames)) {
         colnames(maps) <- colNames
     }
     if (any(!is.element(trusted, colnames(maps)))) {
         stop("trusted must be one of the colNames")
     }
     if (asFile && outName == "") {
         outName <- tempfile("tempFile")
     }
     temp <- apply(maps, 1, doOneRow)
     if (asFile) {
         write.table(x = t(temp), file = outName, quote = FALSE,
             sep = "\t", row.names = FALSE, col.names = FALSE)
         return(outName)
     }
     else {
         return(t(temp))
     }
}
<environment: namespace:AnnBuilder>

If you want to use it, you will either have to call it explicitly using 
the ':::' operator, or maybe you can convince Nianhua that it should be 
exported.

Best,

Jim


> Thanks.
>  
> -Ben
>  
> I'm running R version 2.4.0 on Redhat EW3 Linux and AnnBuilder version 1.12.0.
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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