How to append columns(probe set IDs, locations) to ecoligenome.operon in ecolitk package.
source("http://bioconductor.org/biocLite.R")
## Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for
## help
biocLite("ecolitk")
## BioC_mirror: http://bioconductor.org
## Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version
## 3.1.1.
## Installing package(s) 'ecolitk'
##
## The downloaded binary packages are in
## /var/folders/v0/yw4gp48n09n57hld7sj0d9lm0000gn/T//RtmpPSZqaa/downloaded_packages
library("ecolitk")
data(ecoligenome.operon)
data(ecoligenomeSYMBOL2AFFY)
data(ecoligenomeCHRLOC)
probeset <- mget(ecoligenome.operon$gene.name, ecoligenomeSYMBOL2AFFY, ifnotfound=NA)
loc <- mget(unlist(probeset), ecoligenomeCHRLOC, ifnotfound=NA)
locbegin <- lapply(loc, min)
locend <- lapply(loc, max)
ecoligenome.operon[, "probeset"] <- unlist(probeset)
ecoligenome.operon[, "locbegin"] <- unlist(locbegin)
ecoligenome.operon[, "locend"] <- unlist(locend)
head(ecoligenome.operon)
## gene.name gene.annotation operon.name
## 1 thrA aspartokinase I/homoserine dehydrogenase I thr
## 2 thrB homoserine kinase thr
## 3 thrC threonine synthase thr
## 4 dnaK DNA biosynthesis; heat shock protein dnaK
## 5 dnaJ DNA biosynthesis; heat shock protein dnaK
## 6 yaaC 35K hypothetical ileS-lsp
## operon.comments probeset locbegin locend
## 1 threonine biosynthesis thrA_b0002_st 337 2799
## 2 threonine biosynthesis thrB_b0003_st 2801 3733
## 3 threonine biosynthesis thrC_b0004_st 3734 5020
## 4 DNA biosynthesis dnaK_b0014_st 12163 14079
## 5 DNA biosynthesis dnaJ_b0015_st 14168 15298
## 6 tRNA synthetase & peptidase ribF_b0025_st 21407 22348
write.csv(ecoligenome.operon, file="operon.csv")