[BioC] geneid to gene name conversion

[Paul Shannon]

I was just reminded that mget (an older, classic R approach) has been superseded by Marc Carlson's (modern, intuitive) "select" interface.  Here it is in action:

  select(org.Hs.eg.db, geneIDs, "SYMBOL")
      ENTREZID    SYMBOL
   1      3765     KCNJ9
   2 100126492 TRNAS-CGA
   3 100873237  MTND2P32
   4      9715   FAM131B
   5 100271498  RPL34P22
   6     bogus      <NA>



On Jan 17, 2013, at 6:09 AM, Paul Shannon wrote:

>> 
>> 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
>> 
>> 	[[alternative HTML version deleted]]
>> 
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>