[BioC] multiple annotations with get()?

[James W. MacDonald]

Hi Ed,

I am not sure how this is non-obvious. You tried something and then 
didn't get the result you expected. In my mind, the next obvious step 
is to read the help page for get() to see what the API for that 
function is. And if you had done so, you would have seen:

Description:

     Search by name for an object (‘get’) or zero or more objects
     (‘mget’).

Usage:

     get(x, pos = -1, envir = as.environment(pos), mode = "any",
         inherits = TRUE)

     mget(x, envir = as.environment(-1), mode = "any", ifnotfound,
          inherits = FALSE)

Arguments:

       x: For ‘get’, an object name (given as a character string).
          For ‘mget’, a character vector of object names.


Best,

Jim

On Friday, October 11, 2013 4:08:13 PM, Ed Siefker wrote:
> Thanks, I figured the answer would be something trivial but nonobvious
> like that.  Out of
> curiosity, is there a reason get() isn't designed to "do the right
> thing" if passed a character
> vector of length >1?
>
> On Fri, Oct 11, 2013 at 2:34 PM, Sean Davis <sdavis2 at mail.nih.gov> 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