Hello,
I would like to know if this approach is correct. Briefly, I have a list of targets for a miR and I want to perform GO unsing topGO. TopGO needs a function (geneSel) telling it which genes to choose from the gene set, which is usually the differentially expressed ones. Since I have a list of genes (targets for the miR) I have no expression values and therefore, no sigincancies. So, this is what I did, but I am not sure if is correct:
get all gene names:
mart <- useDataset("hsapiens_gene_ensembl", mart=useMart("ensembl")) all_ensembl_gene_id <- getBM(attributes = "ensembl_gene_id", values = "*", mart = mart)
Select the targets IDs and give them value of 1. The rest of IDs in the set are 0s.
all <- factor(as.integer (all_ensembl_gene_id[,1] %in% targets)) names(all) <- all_ensembl_gene_id[,1]
Perform gene ontology, choosing only targets (1's)
GOdata <- new("topGOdata",ontology = "CC", allGenes = all, geneSel=function(p) p == 1, description ="miR-targets", annot=annFUN.org, mapping="org.Hs.eg.db", ID="Ensembl")
Do you think this is a valid way to perform a GO. I am fairly new to this and I would appriciate your help very much.
Thanks
Thank you for replying.
The vector of gene ids would be my targets, right?
and, do you think that using all gene IDs as background is a valid approach?
Cheers!