Hi, When I tried to use GenomicFeatures, how could I get the gene symbol from the transcripts built from hg19? I had the following commands, and I expected to see names like "TP53", "MMP11", "UBE2E" etc, but instead, I only had the numbers (which did not add much value) when I used the names().
-Kunbin >hg19kg<-makeTranscriptDbFromUCSC(genome="hg19", tablename="knownGene") >GR<-transcripts(hg19kg, vals<-list(tx_chrom="chr1", tx_strand="+")) >GRList<-transcriptsBy(hg19kg, by="gene") > names(GRList)[1:20] [1] "1" "10" "100" "1000" "10000" "100008586" [7] "100008587" "100009676" "10001" "10002" "10003" "100033413" [13] "100033414" "100033415" "100033416" "100033417" "100033420" "100033422" [19] "100033423" "100033424" > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-unknown-linux-gnu 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=C 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] tcltk stats graphics grDevices utils datasets methods [8] base other attached packages: [1] GenomicFeatures_1.0.4 DEGseq_2.0.0 samr_1.28 [4] impute_1.24.0 ShortRead_1.6.2 Rsamtools_1.0.1 [7] lattice_0.19-11 Biostrings_2.16.7 GenomicRanges_1.0.1 [10] IRanges_1.6.8 qvalue_1.22.0 loaded via a namespace (and not attached): [1] Biobase_2.8.0 biomaRt_2.4.0 BSgenome_1.17.1 DBI_0.2-5 [5] grid_2.11.0 hwriter_1.3 RCurl_1.4-3 RSQLite_0.9-2 [9] rtracklayer_1.8.1 tools_2.11.0 XML_3.1-1 > ______________________________________________________________________ The contents of this electronic message, including any attachments, are intended only for the use of the individual or entity to which they are addressed and may contain confidential information. If you are not the intended recipient, you are hereby notified that any use, dissemination, distribution, or copying of this message or any attachment is strictly prohibited. If you have received this transmission in error, please send an e-mail to [email protected] and delete this message, along with any attachments, from your computer. [[alternative HTML version deleted]] _______________________________________________ Bioc-sig-sequencing mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/bioc-sig-sequencing
