

Hi guys,

 

I tried to run
the Filter by Genomic Region example on VariantAnnotation package's filterVcf
vignette page 3, but I kept getting the error message:

 

>
library(VariantAnnotation)

> file.gz <- "somaticVcfBeta-HCC1187-H-200-37-ASM-T1-N1.vcf.gz"

> stopifnot(file.exists(file.gz))

> file.gz.tbi <- paste(file.gz, ".tbi", sep="")

>
file.gz.tbi

[1]
"somaticVcfBeta-HCC1187-H-200-37-ASM-T1-N1.vcf.gz.tbi"

>
file.exists(file.gz.tbi)

[1] FALSE

> if(!(file.exists(file.gz.tbi))

+           
indexTabix(file.gz, format="vcf")

Error: unexpected symbol in:

"if(!(file.exists(file.gz.tbi))

           indexTabix"

 

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   

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          

[5] LC_TIME=English_United States.1252    

 

attached base packages:

[1] parallel 
stats     graphics  grDevices utils     datasets 
methods   base     

 

other attached packages:

[1] VariantAnnotation_1.6.1 Rsamtools_1.12.0        Biostrings_2.28.0      

[4] GenomicRanges_1.12.1   
IRanges_1.18.0         
BiocGenerics_0.6.0     

 

loaded via a namespace (and not attached):

 [1]
AnnotationDbi_1.22.1  
Biobase_2.20.0        
biomaRt_2.16.0        

 [4] bitops_1.0-5           BSgenome_1.28.0        DBI_0.2-5             

 [7]
GenomicFeatures_1.12.0 RCurl_1.95-4.1        
RSQLite_0.11.2        

[10] rtracklayer_1.20.0    
stats4_3.0.0           tools_3.0.0           

[13] XML_3.96-1.1          
zlibbioc_1.6.0        

> 

 


 		 	   		  
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