Hi, When I tried to get the exons sequence, I got an error.. library("BSgenome.Hsapiens.UCSC.hg19") txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene tx_Exons<-exonsBy(txdb) tx1<-tx_Exons[1:3] (seq<-getSeq(Hsapiens,tx1)) Error in .toGRanges(names, strand) : invalid 'names' Any help is apreciated Thank you. [[alternative HTML version deleted]]

Hello, This code works for me in both release and devel. library(GenomicFeatures) library(BSgenome.Hsapiens.UCSC.hg19) library(TxDb.Hsapiens.UCSC.hg19.knownGene) txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene tx_Exons <- exonsBy(txdb) tx1<-tx_Exons[1:3] seq<-getSeq(Hsapiens,tx1) >> seq > DNAStringSetList of length 3 > [["1"]] CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTA GCCCAGACT... > [["2"]] CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTA GCCCAGACT... > [["3"]] CTTGCCGTCAGCCTTTTCTTTGACCTCTTCTTTCTGTTCATGTGTATTTGCTGTCTCTTA GCCCAGACT... What is your sessionInfo()? I've included my below. Valerie > sessionInfo() R version 3.1.0 Patched (2014-04-18 r65405) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] TxDb.Hsapiens.UCSC.hg19.knownGene_2.14.0 [2] BSgenome.Hsapiens.UCSC.hg19_1.3.99 [3] BSgenome_1.32.0 [4] Biostrings_2.32.0 [5] XVector_0.4.0 [6] GenomicFeatures_1.16.2 [7] AnnotationDbi_1.26.0 [8] Biobase_2.24.0 [9] GenomicRanges_1.16.3 [10] GenomeInfoDb_1.0.2 [11] IRanges_1.22.9 [12] BiocGenerics_0.10.0 loaded via a namespace (and not attached): [1] BatchJobs_1.2 BBmisc_1.6 BiocParallel_0.6.1 [4] biomaRt_2.20.0 bitops_1.0-6 brew_1.0-6 [7] codetools_0.2-8 DBI_0.2-7 digest_0.6.4 [10] fail_1.2 foreach_1.4.2 GenomicAlignments_1.0.1 [13] iterators_1.0.7 plyr_1.8.1 Rcpp_0.11.2 [16] RCurl_1.95-4.1 Rsamtools_1.16.0 RSQLite_0.11.4 [19] rtracklayer_1.24.2 sendmailR_1.1-2 stats4_3.1.0 [22] stringr_0.6.2 tools_3.1.0 XML_3.98-1.1 [25] zlibbioc_1.10.0 On 07/30/2014 08:06 AM, Asma rabe wrote: > Hi, > > When I tried to get the exons sequence, I got an error.. > > > library("BSgenome.Hsapiens.UCSC.hg19") > > txdb<-TxDb.Hsapiens.UCSC.hg19.knownGene > > > tx_Exons<-exonsBy(txdb) > > tx1<-tx_Exons[1:3] > > > (seq<-getSeq(Hsapiens,tx1)) > > Error in .toGRanges(names, strand) : invalid 'names' > > Any help is apreciated > Thank you. > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Valerie Obenchain Program in Computational Biology Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, Seattle, WA 98109 Email: vobencha at fhcrc.org Phone: (206) 667-3158