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 _______________________________________________ Bioc-sig-sequencing mailing list Bioc-sig-sequencing@r-project.org https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing