[gwascat] makeCurrentGwascat() fails
0
Entering edit mode
enricoferrero • 570
@enricoferrero-6037
Last seen 5 weeks 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 • 650 views
ADD COMMENTlink
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     
ADD REPLYlink
0
Entering edit mode

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

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 254 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.4