resolveMaps removed from AnnBuilder?
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Wittner, Ben ▴ 290
@wittner-ben-1031
Last seen 6.8 years ago
USA/Boston/Mass General Hospital
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. 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-5106
Last seen 2 days ago
United States
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.
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Wittner, Ben, Ph.D. <wittner.ben at="" ...=""> writes: > > 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. > > 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 ... > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > > Hi, Ben, I have added "resolveMaps" to the NAMESPACE of AnnBuilder. The updated version is 1.13.1, which is available at svn respository now. I am not sure whether "resolveMaps" is a deprecated function or not. Maybe others could help to clarify this part. I only know that the function is not used by any other functions in AnnBuilder, and it was removed from NAMESPACE last November (revision 15047). But anyway, I passed R CMD check after adding "resolveMaps" back to NAMESPACE. So, maybe we can leave it as it. thanks nianhua
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