[Bioc-sig-seq] questions about GenomicFeatures

[Martin Morgan]

On 06/29/2011 04:18 PM, Kunbin Qu wrote:
> 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"

Hi Kunbin

These are ENTREZ gene ids, and you're after (the much more ambiguous) 
SYMBOL identifiers. Use

   nms <- GRList[1:20]
   library(org.Hs.eg.db)
   map <- org.Hs.egSYMBOL
   toTable(map[nms])

or maybe mget(nms, map, ifnotfound=MA) and processing

Martin

>> 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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