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
>


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