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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