Question: [gwascat] makeCurrentGwascat() fails
0
gravatar for enricoferrero
3.6 years ago by
enricoferrero570
Switzerland
enricoferrero570 wrote:

Hello,

I'm trying to generate a current version of the NHGRI/EBI GWAS catalog using makeCurrentGwascat() from the gwascat package and I get this error:

> library(gwascat)

> gwascat <- makeCurrentGwascat()
running read.delim on http://www.ebi.ac.uk/gwas/api/search/downloads/alternative...
formatting gwaswloc instance...
NOTE: input data had non-ASCII characters replaced by '*'.
Error in `[[<-`(`*tmp*`, name, value = numeric(0)) :
  0 elements in value to replace 24454 elements

> gwascat <- makeCurrentGwascat(fixNonASCII=FALSE, genome="GRCh37")
running read.delim on http://www.ebi.ac.uk/gwas/api/search/downloads/alternative...
formatting gwaswloc instance...
Error in `[[<-`(`*tmp*`, name, value = numeric(0)) :
  0 elements in value to replace 24454 elements

Can anyone confirm this behaviour? I'm running R 3.2.2 with gwascat 2.2.0.

Thanks,

Enrico

 

 

 

gwascat • 589 views
ADD COMMENTlink written 3.6 years ago by enricoferrero570
1

I get a warning, but the command works for me:

> gwascat <- makeCurrentGwascat()
running read.delim on http://www.ebi.ac.uk/gwas/api/search/downloads/alternative...
formatting gwaswloc instance... 
NOTE: input data had non-ASCII characters replaced by '*'. done. 
Warning message: 
In gwdf2GRanges(tab, extractDate = as.character(Sys.Date())) : NAs introduced by coercion

That's with today's R-devel and updated packages.

> sessionInfo()
R Under development (unstable) (2016-03-28 r70390)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] gwascat_2.3.6                          
 [2] Homo.sapiens_1.3.1                     
 [3] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [4] org.Hs.eg.db_3.2.3                     
 [5] GO.db_3.2.2                            
 [6] RSQLite_1.0.0                          
 [7] DBI_0.3.1                              
 [8] OrganismDbi_1.13.5                     
 [9] GenomicFeatures_1.23.27                
[10] GenomicRanges_1.23.24                  
[11] GenomeInfoDb_1.7.6                     
[12] AnnotationDbi_1.33.7                   
[13] IRanges_2.5.40                         
[14] S4Vectors_0.9.44                       
[15] Biobase_2.31.3                         
[16] BiocGenerics_0.17.3     
ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Mike Smith4.0k

Thanks for checking - I'll see if updating solves it.

ADD REPLYlink written 3.5 years ago by enricoferrero570
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 141 users visited in the last hour