if(interactive()){
## Makes an organism package for Zebra Finch data.frames:
finchFile <- system.file("extdata","finch_info.txt",package="AnnotationForge")
finch <- read.table(finchFile,sep="\t")
## not that this is how it should always be, but that it *could* be this way.
fSym <- finch[,c(2,3,9)]
fSym <- fSym[fSym[,2]!="-",]
fSym <- fSym[fSym[,3]!="-",]
colnames(fSym) <- c("GID","SYMBOL","GENENAME")
fChr <- finch[,c(2,7)]
fChr <- fChr[fChr[,2]!="-",]
colnames(fChr) <- c("GID","CHROMOSOME")
finchGOFile <- system.file("extdata","GO_finch.txt",package="AnnotationForge")
fGO <- read.table(finchGOFile,sep="\t")
fGO <- fGO[fGO[,2]!="",]
fGO <- fGO[fGO[,3]!="",]
colnames(fGO) <- c("GID","GO","EVIDENCE")
makeOrgPackage(gene_info=fSym, chromosome=fChr, go=fGO,
version="0.1",
maintainer="Some One <so@someplace.org>",
author="Some One <so@someplace.org>",
outputDir = ".",
tax_id="59729",
genus="Taeniopygia",
species="guttata",
goTable="go")
## then you can call install.packages based on the return value
install.packages("./org.Tguttata.eg.db", repos=NULL)
}
Run the code above in your browser using DataCamp Workspace