Report 02/10/12

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)