ying chen | 6 May 16:47 2013

VariantAnnotation error with readVcf in Windows 7

Hi guys, I tried a sample with Variant Annotation's eadVcf. I ran the code successfully in Linux (OK I had
some warnings regarding " unpackVcf field '..': NAs introduced by coercion"). But when I tried the same
code in R3.0.0 in windows 7, I got the error message: > for(i in 1:length(vcflist1)){
         indexTabix(vcflist1[i], format="vcf")
         vcf <- readVcf(TabixFile(vcflist1[i]), "hg19", params)
         outputfile=paste(sub(".vcf.gz","",vcflist1[i]),"_test.vcf",sep="")
         writeVcf(vcf,outputfile)
         bgzip(outputfile, overwrite=TRUE)
         indexTabix(paste(outputfile,".gz",sep=""), format="vcf")
         rm(vcf)
         rm(outputfile)
   }
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘readVcf’ for signature ‘"TabixFile", "character",
"standardGeneric"’ What did I do wrong? Thanks a lot for the help! Ying
> sessionInfo()
R version 3.0.0 (2013-04-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   
LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     other attached packages:
 [1] VariantAnnotation_1.6.5 Rsamtools_1.12.2        Biostrings_2.28.0       GenomicRanges_1.12.2   
 [5] IRanges_1.18.0          org.Hs.eg.db_2.9.0      RSQLite_0.11.3          DBI_0.2-6              
 [9] AnnotationDbi_1.22.5    Biobase_2.20.0          BiocGenerics_0.6.0      BiocInstaller_1.10.1   loaded via a
namespace (and not attached):
 [1] biomaRt_2.16.0         bitops_1.0-5           BSgenome_1.28.0        GenomicFeatures_1.12.1 RCurl_1.95-4.1        
 [6] rtracklayer_1.20.2     stats4_3.0.0           tools_3.0.0            XML_3.96-1.1           zlibbioc_1.6.0        
> 

 		 	   		  
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