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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