## ----setup, echo=FALSE-------------------------------------------------------- library(knitr) options(width=80) ## ----wrap-hook, echo=FALSE---------------------------------------------------- hook_output = knit_hooks$get('output') knit_hooks$set(output = function(x, options) { # this hook is used only when the linewidth option is not NULL if (!is.null(n <- options$linewidth)) { x = knitr:::split_lines(x) # any lines wider than n should be wrapped if (any(nchar(x) > n)) x = strwrap(x, width = n) x = paste(x, collapse = '\n') } hook_output(x, options) }) ## ----makeOrgPackageFromNCBI, eval=FALSE--------------------------------------- # library(AnnotationForge) # makeOrgPackageFromNCBI(version = "0.1", # author = "Some One ", # maintainer = "Some One ", # outputDir = ".", # tax_id = "59729", # genus = "Taeniopygia", # species = "guttata") ## ----makeOrgPackage, eval=FALSE----------------------------------------------- # ## Makes an organism package for Zebra Finch data.frames: # finchFile <- system.file("extdata","finch_info.txt", # package="AnnotationForge") # finch <- read.table(finchFile,sep="\t") # # ## Now prepare some data.frames # 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") # # ## Then call the function # makeOrgPackage(gene_info=fSym, chromosome=fChr, go=fGO, # version="0.1", # maintainer="Some One ", # author="Some One ", # 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)