OPERON human v3 library
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
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
Annotation GO Annotation GO • 481 views
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