[Bioc-devel] UniProt.ws: Error in .mergeList when mapping to UNIPROTKB

Thomas Dybdal Pedersen thomasp85 at gmail.com
Fri May 24 15:04:27 CEST 2013


When trying to map from a vector of refseq accessions to uniprot id's I get an error:

refseq <- c("YP_139402", "YP_141320", "YP_820357", "YP_006002448", "YP_006040776", 
"YP_006340074", "YP_006340075", "YP_138830", "YP_819836", "YP_006001858"

select(UniProt.ws, keys=refseq, keytype="REFSEQ_PROTEIN", cols=c('UNIPROTKB'))

I have traced the error back to .mergeList. The problem seems to be that when mapping to UNIPROTKB a data frame with two columns named ACC+ID is produced making the by='ACC+ID' argument in merge() ambiguous.

The easy fix seems to be to only use 'ACC+ID' for internally keeping track of the mapping and use another name for the UNIPROTKB id?


Thomas Pedersen, PhD student at Technical University of Denmark

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