[BioC] geneid to gene name conversion

[Paul Shannon]

> 
> I am looking for a way to convert geneid to gene name. 

Hi Matt,

This might be what you need:

biocLite("org.Hs.eg.db")
library(org.Hs.eg.db)
  # some sample entrez geneIDs; you will have your own source for these
geneIDs <- c("3765","100126492", "100873237", "9715","100271498", "bogus")  
mget(geneIDs, org.Hs.egSYMBOL, ifnotfound=NA)
$`3765`
[1] "KCNJ9"

$`100126492`
[1] "TRNAS-CGA"

$`100873237`
[1] "MTND2P32"

$`9715`
[1] "FAM131B"

$`100271498`
[1] "RPL34P22"

$bogus
[1] NA

 - Paul


On Jan 16, 2013, at 8:11 AM, Matthew Liebers wrote:

> I am looking for a way to convert geneid to gene name.  Specifically, I am
> calling for variants and then using VariantAnnotation to output using a
> predictCoding() function that gives the following columns:
> "seqnames"    "ranges"       "strand" | "paramRangeID"
> "varAllele"       "CDSLOC"              "PROTEINLOC"   "QUERYID"
> "TXID"     "CDSID"      "*GENEID*"   "CONSEQUENCE"       "REFCODON"
> "VARCODON"         "REFAA"         "VARAA".
> 
> I am interested in gene name moreso than GENEID and so I have been looking
> at how to do this including using the biomaRt package, but I was wondering
> whether anyone knew about this.  Thanks in advance!
> 
> Matt
> 
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