[BioC] resolveMaps removed from AnnBuilder?
James W. MacDonald
jmacdon at med.umich.edu
Sun Oct 15 15:57:05 CEST 2006
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.
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at stat.math.ethz.ch
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
--
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
**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.
More information about the Bioconductor
mailing list