Entering edit mode
Lyudmila Mikhaylova
▴
20
@lyudmila-mikhaylova-1352
Last seen 11.2 years ago
Hello,
I was trying the script from "Basic Functions of
AnnBuilder" manual and encountered problem on the line
ug <- UG(srcUrl=ugUrl,...
Error: couldn't find function "UG".
Later on I've got same error message for parseData
function.
HTML help file contains descriptions for both functions.
Please help me to solve this problem.
Script and session info:
library(AnnBuilder)
pkgpath <- .find.package("AnnBuilder")
docFiles <-
file.path(pkgpath,c("TITLE","DESCRIPTION","INDEX"))
headers <- c("","Description:\n\n",,"Index:\n\n")
footers <- c("\n","\n","")
for (i in which(file.exists(docFiles))) {
writeLines(headers[i],sep="")
writeLines(readLines(docFiles[i]) )
writeLines(footers[i],sep="")
}
geneNMap <-
matrix(c("32468_f_at","D90278;M16652","32469_at","L00693",
"32481_at","AL031663","33825_at","X68733",
"35730_at","X03350","36512_at","L32179",
"38912_at","D90042","38936_at","M16652",
"39368_at","AL031668"),ncol=2,byrow=T)
write.table(geneNMap,file="geneNMap",sep="\t",quote=F,
row.names=F,col.names=F)
geneNMap
makeSrcInfo()
srcObjs <- list()
egUrl <-
"http://www.bioconductor.org/datafiles/wwwsources"
ugUrl <-
"http://www.bioconductor.org/datafiles/wwwsources/Ths.data.gz"
eg <-
EG(srcUrl=egUrl,parser=file.path(pkgpath,"scripts","gbLLParser"),baseF
ile="geneNMap",
accession="Tll_tmpl.gz",built="N/A",fromWeb=T)
ug <-
UG(srcUrl=ugUrl,parser=file.path(pkgpath,"scripts","gbUGParser"),baseF
ile="geneNMap",
organism="Homo sapiens",built="N/A",fromWeb=T)
srcObjs[["eg"]] <- eg
llMapping <- parseData(eg,eg at accession)
sessionInfo()
R version 2.1.0, 2005-04-18, i386-pc-mingw32
attached base packages:
[1] "tools" "methods" "stats" "graphics"
"grDevices" "utils"
[7] "datasets" "base"
other attached packages:
AnnBuilder annotate XML Biobase
"1.5.31" "1.5.16" "0.97-7" "1.5.12"
Lyudmila Mikhaylova, Ph.D
Research Associate
Tufts University School of Medicine
