Question

[gwascat] makeCurrentGwascat() fails

0

Entering edit mode

enricoferrero ▴ 660

@enricoferrero-6037

Last seen 3.1 years ago

Switzerland

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 • 1.5k views

ADD COMMENT • link 8.7 years ago enricoferrero ▴ 660

1

Entering edit mode

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