[BioC] OPERON human v3 library

[Nianhua Li]

Hi, Morten,

You can build one yourself:

1. Download the annotation xls file from
http://microarray.genome.duke.edu/spotted-arrays/available-arrays
It is under "List of Genes".

2. Save the xls file as csv file (say "anno.csv"), and extract the oligo_id to
Genbank mapping from it:

anno <- read.csv("anno.csv", header=T, stringsAsFactors=F)
res <- anno[,c(3, 10)]
na_id <- which(res[,1]=="")
res <- res[-na_id, ]
na_acc <- which(res[,2]=="")
res[na_acc, 2] <- "NA"
res <- paste(res[,1], res[,2], sep="\t", collapse="\n")
cat(res, file="operon_human_v3_gb.txt")

3. Create metadata package:

library(AnnBuilder)
operon <- function(pkgPath, version) {
    ABPkgBuilder(baseName="operon_human_v3_gb.txt",
                 baseMapType="gb",
                 pkgName="OperonHumanV3",
                 pkgPath=pkgPath,
                 organism="Homo sapiens",
                 version=version,
                 author=list(
                   authors="YourName",
                   maintainer="YourName <youremail at email.com>"
                   )
                 )
}
operon(getwd(), "1.1.0")

Make sure your GO is up-to-date. You can use "biocLite" to get it.

I just built one. If you can't create it yourself, I can at least email it to
you. But it will be better to build it yourself so that you can modify/update it
as you want. Good luck!

nianhua