Question: Select in UniProt.ws not working?
0
gravatar for sarah.sandmann
3.3 years ago by
Germany
sarah.sandmann0 wrote:

Hi,

I am using UniProt.ws for the first time. It looks great, but it seems as if the select-function (which I really need) is not properly working for me. I just tried the examplary code and this is what I do/get:

> library(UniProt.ws)
> up<-UniProt.ws(taxId=9606)
> keys <- c("1","2")
> columns <- c("PDB","UNIGENE","SEQUENCE")
> kt <- "ENTREZ_GENE"
> res <- select(up, keys, columns, kt)
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217,V9HWD8,P01023
Fehler in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  Objekt '.resort' nicht gefunden

It would be great, if anyone could help me!

Thanks!

Sarah

 

uniprot.ws select • 592 views
ADD COMMENTlink modified 3.3 years ago by Martin Morgan ♦♦ 24k • written 3.3 years ago by sarah.sandmann0

Works for me now

> suppressPackageStartupMessages(library(UniProt.ws))
> up <- UniProt.ws(taxId=9606)
> keys <- c("1", "2")
> columns <- c("PDB", "UNIGENE", "SEQUENCE")
> kt <- "ENTREZ_GENE"
> res <- select(up, keys, columns, kt)
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217,V9HWD8,P01023
'select()' returned 1:many mapping between keys and columns
> str(res)
'data.frame':    8 obs. of  4 variables:
 $ ENTREZ_GENE: chr  "1" "1" "2" "2" ...
 $ PDB        : chr  NA NA "1BV8" "2P9R" ...
 $ UNIGENE    : chr  "Hs.709582" "Hs.529161" "Hs.212838" "Hs.212838" ...
 $ SEQUENCE   : chr  "MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQLFKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPWLSMAPVS"| __truncated__ "MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQLFKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPWLSMAPVS"| __truncated__ "MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETTEKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAENDVLHCVAFAVPKSSSNEEVMFLTVQVKGPTQEFKKRTTVMVKNEDS"| __truncated__ "MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETTEKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAENDVLHCVAFAVPKSSSNEEVMFLTVQVKGPTQEFKKRTTVMVKNEDS"| __truncated__ ...

using

> sessionInfo()
R version 3.3.1 Patched (2016-08-02 r71022)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

locale:
 [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8    
 [5] LC_MONETARY=en_GB.UTF-8    LC_MESSAGES=en_GB.UTF-8   
 [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] UniProt.ws_2.13.0   BiocGenerics_0.19.2 RCurl_1.95-4.8     
[4] bitops_1.0-6        RSQLite_1.0.0       DBI_0.4-1          

loaded via a namespace (and not attached):
[1] compiler_3.3.1       IRanges_2.7.12       tools_3.3.1         
[4] msdata_0.12.1        Biobase_2.33.0       AnnotationDbi_1.35.4
[7] S4Vectors_0.11.10    stats4_3.3.1       
ADD REPLYlink written 3.3 years ago by Laurent Gatto1.2k

Are your packages in sync? Test this with

BiocInstaller::biocValid()

If so, EDIT your question to include the output of the command

traceback()

immediately after the error. And also include the output of the command

sessionInfo()
ADD REPLYlink written 3.3 years ago by Martin Morgan ♦♦ 24k

Thanks a lot for your answers.

It turned out, we had a version problem considering Bioconductor, various packages and different users.

Everything is working as it should right now. Thanks agian!

ADD REPLYlink written 3.3 years ago by sarah.sandmann0
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