Hi,
I am working on wheat RNA seq data.I have found differential expressed genes in wheat. Now I want to do gene ontology by using GOseq R package.
This package take the genome ids as given in manual
pwf=nullp(genes,"hg19","ensGene")
hg19 is for human. but I could not found this type of genome id for Wheat. Can anyone tell me which one is used for wheat?
You can use supportedOrganisms() to get a list of genomes that are supported and their IDs. However, I would be surprised if goseq had this available for wheat, in which case you'll have to supply the bias.data and the category mappings yourself. See section 5 of the GOSeq manual. In this case you'd supply the bias.data to nullp directly, rather than via genome and gene id type:
You can use bioMart. Go to plants.ensembl.org and select bioMart, Wheat as the the genome, and then under features/external you can select GO accession.
Where we can get category mappings as these are not available
You can use bioMart. Go to plants.ensembl.org and select bioMart, Wheat as the the genome, and then under features/external you can select GO accession.