[BioC] problem with IGH genes in org.Hs.egCHRLOC

Marc Carlson mcarlson at fhcrc.org
Tue Nov 1 23:08:50 CET 2011

Hi Francois,

The CHRLOC mappings are based on the data from UCSC, but in order to 
find a match to "28473",  the UCSC knownToLocusLink table that we 
download from UCSC every release has to have an entry in it for 
"28473".  Unfortunately, it doesn't.  In fact, none of the NCBI linked 
UCSC resources seems to have any entries for entrez gene "28473", which 
means that you are probably stuck looking for this value by using 
another resource (one that is not based on UCSC).  So I think you really 
do want to try biomart in this particular case.


On 10/31/2011 05:53 PM, Francois Pepin wrote:
> Hi everyone,
> I'm trying to get information about the IGH alleles and i'm getting strange results from org.Hs.eg.db.
> For example, if we use IGHV1-3 (located at chr14, starting around 106,471,246 on NCBI&  Ensembl websites):
>> library(org.Hs.eg.db)
>> get("28473",org.Hs.egSYMBOL)
> [1] "IGHV1-3"
>> get("28473",org.Hs.egCHRLOC)
> [1] NA
> I guess I could use biomart for these, but I'm surprised that org.Hs.egCHRLOC would not work for these genes. A quick test with other genes show results that are consistent with the data on the NCBI&  Ensembl websites. I've also tested it on the devel version downloaded today (org.Hs.eg.db_2.5.0) with the same results.
>> sessionInfo()
> R version 2.13.1 (2011-07-08)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> other attached packages:
> [1] org.Hs.eg.db_2.5.0   RSQLite_0.9-4        DBI_0.2-5
> [4] AnnotationDbi_1.14.1 Biobase_2.12.2
> François Pepin
> Scientist
> Sequenta, Inc.
> 400 E. Jamie Court, Suite 301
> South San Francisco, CA 94080
> 650 243 3929 p
> francois.pepin at sequentainc.com
> www.sequentainc.com
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