<p>From the <code>UniProt.ws</code> <a href="https://bioconductor.org/packages/release/bioc/manuals/UniProt.ws/man/UniProt.ws.pdf" rel="nofollow noreferrer">manual</a>:</p>

<blockquote>
  <p><code>columns</code> shows which kinds of data can be returned for the
  <code>UniProt.ws</code> object.</p>
</blockquote>

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

<p>And <a href="https://bioinformatics.stackexchange.com/questions/9093/how-to-retrieve-the-subcellular-location-info-from-uniprot">here</a> is a related question.</p>

CC BY-SA 4.0
2019-11-11T19:42:59.980Z
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)`
Mahasish
CC BY-SA 4.0
2019-11-09T14:06:24.417Z
2019-11-09T14:06:24.417Z
haci
<p>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.</p>

<p>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).</p>

CC BY-SA 4.0
2019-11-11T19:38:44.703Z
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. https://support.bioconductor.org/p/78380/ . res <- select(up, "P35579", "SUBCELLULAR-LOCATIONS", "UNIPROTKB")
Mahasish
CC BY-SA 4.0
2019-11-09T07:43:07.087Z
2019-11-09T07:43:07.087Z
dc37
<p>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.</p>

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

<p>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.</p>

<r><bioconductor><uniprot><rstudio>
How can I find all the columns available in UniProt.ws package for R?
# How can I find all the columns available in UniProt.ws package for R?

(Asked by: username_0 on 2019-11-09)

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.

**Tags:** r, bioconductor, uniprot, rstudio

---

## 2 answers

### Answer by username_1 on 2019-11-09. Score: 1 | Accepted answer

From the `UniProt.ws` [manual](https://bioconductor.org/packages/release/bioc/manuals/UniProt.ws/man/UniProt.ws.pdf):

> `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](https://bioinformatics.stackexchange.com/questions/9093/how-to-retrieve-the-subcellular-location-info-from-uniprot) is a related question.

> **Comments:**
> **username_0**: 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)`  

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### Answer by username_2 on 2019-11-09. Score: 1

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).

> **Comments:**
> **username_0**: 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. https://support.bioconductor.org/p/78380/ . res <- select(up, "P35579", "SUBCELLULAR-LOCATIONS", "UNIPROTKB")  

---

