I need your help for Goseq R code for gene ontology enrichment analysis for differentially expressed gene identified by DESeq2.
I got the differentially expressed genes and I can also download the mapping file from biomart for all the rice gene ID like below:
Gene stableID Transcript stable ID GO term accession BGIOSGA013239 BGIOSGA013239-TA GO:0009098 BGIOSGA013239 BGIOSGA013239-TA GO:0003862 BGIOSGA013239 BGIOSGA013239-TA GO:0009082 BGIOSGA013239 BGIOSGA013239-TA GO:0016616 BGIOSGA013239 BGIOSGA013239-TA GO:0051287
Goseq code: d <- read.csv("deseq2res.csv", header=T, row.names=1) all_genes <- row.names(d) DE_genes <- all_genes[d$padj<0.05]
I am not sure how should I proceed further after this?
I am not able to understand how should I get the genes.vector and length.vector.names for the below code and then GO_data.frame?
pwf <- nullp(genes.vector,bias.data=length.vector.names) head(pwf) # calculate GO enrichment using default method GO.WALL <- goseq(pwf, gene2cat=GO_data.frame)