PSICQUIC addGeneInfo invalid attribute names
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@anaisbaudot-7935
Last seen 6.1 years ago
France

Dear all,

I have a problem with the PSICQUIC package while mapping gene name synonyms. Here are the command lines :

# data fetching

tbl.big <- PSICQUIC::interactions(psicquic, species="9606",provider=DB, type="direct interaction”)

 

#mapping

idMapper <- IDMapper("9606")

tbl.big.2 <- addGeneInfo(idMapper,tbl.big)

 

However, the last step now fails with the message:

 

Error in getBM(filters = filter, values = uniprots, attributes = columns,  : 

Invalid attribute(s): uniprot_swissprot_accession 

Please use the function 'listAttributes' to get valid attribute names

 

I cannot figure out what had changed, since this was working well before, and since the example provided in the vignette is also fine...

 

Thanks for your help

 

Anaïs

psicquic • 791 views
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pshannon ▴ 90
@pshannon-6931
Last seen 5.6 years ago
United States

Hi Anaïs,

Biomart changed the name of this attribute to simply "uniprot_swissprot" about the first of the year.  We discovered this -- just as you did! -- and made the fix in PSICQUIC version 1.5.7.

biocLite("PSICQUIC")   ought to solve the problem.

- Paul

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@anaisbaudot-7935
Last seen 6.1 years ago
France

Many thanks, I should have thought about updating before complaining!!

 

Anaïs

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