Bioconductor Libraries to learn
http://www.bioconductor.org/packages/2.10/bioc/vignettes/topGO/inst/doc/topGO.pdf
Keggapi
Updated R to version 2.15
echo "deb http://cran.mirrors.hoobly.com/bin/linux/ubuntu precise/" >> /etc/apt/sources.list gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 gpg -a --export E084DAB9 | sudo apt-key add -
Installed
http://www.omegahat.org/RCurl/FAQ.html
Biomart
library(KEGGSOAP)
genes <- get.genes.by.pathway(“path:hsa04340”)
#for each gene
genes <- sub(“(hsa:)”, “”, genes)
length(genes)
genes
#biomart
library(“biomaRt”)
ensembl = useMart(“ensembl”,dataset=”hsapiens_gene_ensembl”)
goids = getBM(attributes=c(‘entrezgene’,’go_id’), filters=’entrezgene’, values=genes, mart=ensembl)