I would like to use UniProt.ws to convert UniProt ids to SGD ids for Saccharomyces cerevisiae but my attempts so far have resulted in the error:
Error in .select(x, keys, columns, keytype) :
No data is available for the keys provided.
Here is a minimal example, where I attempt to convert "I2HB52". The expected answer is "YBR056W-A" (see http://www.uniprot.org/uniprot/I2HB52 ).
library(UniProt.ws) taxId(UniProt.ws) <- 4932 species(UniProt.ws) res <- select(x=UniProt.ws, keys="I2HB52", columns="SGD", keytype="UNIPROTKB")
Is this particular conversion currently possible using UniProt.wd? Different choices for 'columns' also result in the same error.
Thanks in advance,
Joseph Barry
Session Info:
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
locale:
[1] en_IE.UTF-8/en_IE.UTF-8/en_IE.UTF-8/C/en_IE.UTF-8/en_IE.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods
[7] base
other attached packages:
[1] UniProt.ws_2.6.0 RCurl_1.95-4.5 bitops_1.0-6 RSQLite_1.0.0
[5] DBI_0.3.1
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.28.1 Biobase_2.26.0 BiocGenerics_0.12.1
[4] GenomeInfoDb_1.2.4 IRanges_2.0.1 parallel_3.1.2
[7] S4Vectors_0.4.0 stats4_3.1.2 tools_3.1.2
I made a small change to the devel version of UniProt.ws, and it now works:
I'll check with Marc Carlson about adding this change to the package.