[BioC] altrenative gene symbols

[Marc Carlson]

Hi Burak,

You can always use the ALIAS2EG and the SYMBOL mappings in the organism
annotation packages.  So for example using the human package org.Hs.eg.db:

library(org.Hs.eg.db)
IDs = c("ACS1","LACS","FACL1","FACL2","LACS1","LACS2","ACSL1")
#1st use ALIAS2EG to get entrez gene IDs for these
EGs = mget(IDs, org.Hs.egALIAS2EG, ifnotfound=NA)
#have a look at these:
EGs
#At this point you can already see that these all map to the same gene ID
#BUT, you can get the most popular symbol by using the SYMBOL mapping:
mget(as.character(EGs[1]),org.Hs.egSYMBOL, ifnotfound=NA)

Hope this helps,

  Marc




burak kutlu wrote:
> Hi 
> Is there a way to convert non-HUGO gene symbol identifiers to entrez gene or other ids?
> Example:
> ACSL1 aka ACS1; LACS; FACL1; FACL2; LACS1; LACS2; ACSL1
> Thanks in advance
> -burak
>
>
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