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
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