> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] GenomicFeatures_1.10.0  AnnotationDbi_1.20.0
Biobase_2.18.0          VariantAnnotation_1.4.6 Rsamtools_1.10.1
Biostrings_2.26.2       GenomicRanges_1.10.2    IRanges_1.16.3
BiocGenerics_0.4.0      vimcom_0.9-5            setwidth_1.0-3
[12] colorout_0.9-9

loaded via a namespace (and not attached):
 [1] BSgenome_1.26.1    DBI_0.2-5          RCurl_1.95-1.1
RSQLite_0.11.2     XML_3.95-0.1       biomaRt_2.14.0     bitops_1.0-4.1
parallel_2.15.1    rtracklayer_1.18.0 stats4_2.15.1      tools_2.15.1
zlibbioc_1.4.0


On Fri, Feb 1, 2013 at 12:41 AM, sun <fireflysrb@gmail.com> wrote:

> Hi
>
> I put locateVariants() in a test() function, save test() in "test.R" file.
> see bellow scripts,
>
> In "test.R" file,
> test <-function() {
>    vcf <-readVcf("var.raw.vcf","Arabidopsis")
>    rd <-rowData(vcf)
>    txdb <-loadDb("Arabidopsis.sqlite")
>    allvar <- locateVariants(rd,txdb, AllVariants())
> }
>
> Then I open R to run the following scripts,
>
> source("test.R")
> library(VariantAnnotation)
> library(GenomicFeatures)
> test()
>
> I got an error "Error in isActiveSeq(x) :
>   error in evaluating the argument 'x' in selecting a method for function
> 'isActiveSeq': Error: object 'txdb' not found"
>
> However, when I run the following scripts directly (don't put in a
> function) ,the locateVariants() works.
> vcf <-readVcf("var.raw.vcf","Arabidopsis")
> rd <-rowData(vcf)
> txdb <-loadDb("Arabidopsis.sqlite")
> allvar <- locateVariants(rd,txdb, AllVariants())
>
> How can I load txdb object correctly so I can call locateVariants() in
> function?
>
> Thanks,
>
> Rebecca
>

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