[BioC] Error when try VariantAnnotation filterVcf vignette example

[Martin Morgan]

On 04/11/2013 11:06 AM, ying chen wrote:
>
>
> 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?

A simple typo in the vignette

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

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

Martin

>
>
>
> 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
>
>>
>
>
>
>
>   		 	   		
> 	[[alternative HTML version deleted]]
>
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