I have a list of HGNC IDs and wanted to map it to uniprot.swissprot ID.
The tools I have used so far are
- David tool for conversion of IDs,
- Biomart (R package) and
- Mygene.info (R package)
But the problem with the first two tools (David and Biomart) is that they accept only smaller gene list as an input and I have 60,000 list of genes. So, I have also tried Mygene.info as an R package (As I have better understanding of R than python or any other programming languages). But when I try to give a gene list as an input in (mygene) package,
res <- queryMany(c('1053_at', '117_at', '121_at', '1255_g_at', '1294_at'),scopes='reporter', species='human')
it shows
Error: is.request(y) is not TRUE
Why is the error showing, whenever I am inputting a gene-list. Please help me figure out where the problem is and how it can be solved?
Thanks in advance.
1 answer
Have you tried the UniProt IDmapping tool? http://www.uniprot.org/uploadlists
It works with HGNC identifiers (e.g. HGNC:9884) or gene symbols (e.g. RB1), however not with Affymetrix probeset identifiers.
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Elisabeth Gasteiger
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I'd suggest sticking with biomaRt and just getting all genes. You can then match up or filter your results in R. Or am I misunderstanding your problem?
I'm suggesting not supplying any filter values. Just have biomaRt pull the data for all the genes.
Yeah just ran biomaRt without any filters (
ID <- getBM(attributes= c("hgnc_symbol", "uniprot_genename","uniprot_swissprot"),mart= mart)). Got a list of 35353 genes. So, now I have to map it with my gene list, right? Correct me if I am wrong. Thanks a lot. It solved the problem.In R, this is a subsetting, match(), or merge() operation that will likely take just a second or two to run.
If you don't mind could you please add your answer with an example because I dont want to leave any gap in my understanding.
I think it needs to be pointed out that you're not passing in a gene list there, they're not HGNC identifiers, they're Affymetrix probeset identifiers, which is not really the same thing at all...