[BioC] multiple annotations with get()?

[Sean Davis]

On Fri, Oct 11, 2013 at 3:53 PM, James W. MacDonald <jmacdon at uw.edu> wrote:
> You might also consider using select(), which is the newfangled way to do
> things:
>
>> z <- c("SFRP2","MGP","COL10A1","MSRB3")
>> select(org.Hs.eg.db, z, "ENTREZID","SYMBOL")
>
>   SYMBOL ENTREZID
> 1   SFRP2     6423
> 2     MGP     4256
> 3 COL10A1     1300
> 4   MSRB3   253827

Definitely the better way to go.

Sean


> On Friday, October 11, 2013 3:34:45 PM, Sean Davis wrote:
>>
>> On Fri, Oct 11, 2013 at 3:31 PM, Ed Siefker <ebs15242 at gmail.com> wrote:
>>>
>>> I have a list of gene symbols I want to convert into entrez ids.
>>> For example, I have a txt file with these symbols:
>>>
>>> SFRP2
>>> MGP
>>> COL10A1
>>> MSRB3
>>>
>>> I've loaded Biobase, annotate, and org.Hs.eg.db and done the following:
>>>
>>> symb<- read.table("example.txt",stringsAsFactors=FALSE)
>>>>
>>>> get(symb, org.Hs.egSYMBOL2EG)
>>
>>
>> Hi, Ed.
>>
>> You may want to use mget (multiple get) instead.
>>
>> Sean
>>
>>> Error in .checkKeysAreWellFormed(keys) :
>>>    keys must be supplied in a character vector with no NAs
>>>>
>>>> class(symb[[1]])
>>>
>>> [1] "character"
>>>>
>>>> length(symb[[1]])
>>>
>>> [1] 4
>>>>
>>>> get(symb[[1]], org.Hs.egSYMBOL2EG)
>>>
>>> [1] "6423"
>>>
>>> Why is get() only giving me one entrez ID?  Shouldn't it give me a vector
>>> of 4 entrez IDs when I pass it a vector of 4 gene symbols?
>>>
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>>
>>
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>
>
> --
> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
> 4225 Roosevelt Way NE, # 100
> Seattle WA 98105-6099
>
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