Question: GOSeq with unsupported organism (Arabidopsis) and retrieving gene IDs from enriched GO categories
gravatar for Dale Richardson
4.8 years ago by
Dale Richardson30 wrote:
Hi All, I'm currently working on a differential gene expression analysis and I've used GOSeq to find enriched GO categories, just like what is mentioned here ( 7df4/ ), except I am using a non-supported organism (Arabidopsis). I've come to the exact point in the analysis as Fernando has in the above link, where I would like to extract all gene IDs associated with the enriched GO terms in my DE analysis. My question is, how can I do this with a non-supported organism? For a supported organism, the process looks to be straight forward.. but for an unsupported genome and for a newbie in R, the process isn't so easy.. This is some of the code that got me to where I am now. #calculate pwf function pwf = nullp(genes, tairgo <- read.table("ATH_GO_GOSLIM.txt", header=F, sep="\t", fill=T) #read in GO Categories File GO.wall <- goseq(pwf, gene2cat=tairgo[,c(1,6)]) # get ID and GO columns only from tairgo GO.samp <- goseq(pwf, gene2cat=tairgo[,c(1,6)], method="Sampling",repcnt=1000) enriched.GO = GO.wall$category[p.adjust(GO.wall$over_represented_pvalue, method = "BH") < 0.05] enriched.sampgo = GO.samp$category[p.adjust(GO.wall$over_represented_pvalue, method = "BH") < 0.05] What I've been thinking of doing is looping through my enriched GO terms vector and finding all gene IDs that have matching GO terms in "tairgo". However, is there a better way to do this using one of the functions built into GOSeq? Thanks so much for your valuable input!! -- Dale Richardson, Ph.D. Laboratory of Plant Molecular Biology Instituto Gulbenkian de Ci?ncia Rua da Quinta Grande, 6 2780-156 Oeiras Portugal Tel: +351 214 464 647
ADD COMMENTlink written 4.8 years ago by Dale Richardson30
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 195 users visited in the last hour