[Bioc-sig-seq] extract 3UTR using GenomicFeatures package

[Jason Lu]

Hi,

I would like to extract 3'UTR for a list of refseq NMs using the
GenomicFeatures pkg.  However I encountered the following error.

Here is what I have:

===================
library(GenomicFeatures)
txdb  = loadFeatures("txdb.hg19.refGene.sqlite")
threeutr.tx = threeUTRsByTranscript(txdb, use.names=TRUE)


library("BSgenome.Hsapiens.UCSC.hg19")
> extractTranscriptsFromGenome(Hsapiens,threeutr.tx[1:4])
Error in .normargExonStartsOrEnds(exonStarts, "exonStarts") :
  'exonStarts' must be a list of integer vectors, an IntegerList object,
  or a character vector where each element is a comma-separated list of
  integers

> sessionInfo()
R version 2.13.0 Under development (unstable) (2011-01-20 r54055)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] GenomicFeatures_1.3.14             BSgenome.Hsapiens.UCSC.hg19_1.3.17
[3] BSgenome_1.19.5                    Biostrings_2.19.17
[5] GenomicRanges_1.3.25               IRanges_1.9.27

loaded via a namespace (and not attached):
[1] Biobase_2.11.10     DBI_0.2-5           RCurl_1.5-0
[4] RSQLite_0.9-4       XML_3.2-0           biomaRt_2.7.1
[7] rtracklayer_1.11.12 tools_2.13.0


Thanks for checking.

Jason