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I am trying to find the subcellular localization of my 10,000 proteins using UniProt.ws package for R. However, I am unable to find all the columns available for query.

I used another package named Bioconductor which had easy way to lookup all the columns available using COLUMNS(org.Hs.eg.db)

I tried reading the documentation and couldn't find anything which can output subcellular localization. I am new to this field, any help is appreciated.

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2 Answers 2

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From the UniProt.ws manual:

columns shows which kinds of data can be returned for the UniProt.ws object.

So, you will need to go over the output of columns(your_uniprotws_object) if it includes the data type you are looking for.

And here is a related question.

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  • $\begingroup$ Thank you. It worked for me now with this code: up <- UniProt.ws(taxId=9606) keys <- c("4957","81551") columns <- c("PDB","GENES","SUBCELLULAR-LOCATIONS") select(up, keys, columns, kt) $\endgroup$
    – Mahasish
    Commented Nov 11, 2019 at 19:42
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Do you have a small sample of the proteins you are looking for and what you have tried so far in R using Uniprot.ws ? (including output of it), it could be helpful to identify your problem and how to solve it.

Personally, I would rather consider Bioconductor as a platform for providing R packages dedicated to bioinformatics than a package to analyze data (but it's my opinion, maybe I'm wrong).

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  • $\begingroup$ I have 10000 proteins which I am looking for sub-cellular localization. I tried to find the columns available in UniProt.ws using COLUMNS(UniProt.ws) but it didn't work. Finally, I looked into Bioconductor as you said and found the answer. support.bioconductor.org/p/78380 . res <- select(up, "P35579", "SUBCELLULAR-LOCATIONS", "UNIPROTKB") $\endgroup$
    – Mahasish
    Commented Nov 11, 2019 at 19:38

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