[BioC] multiple annotations with get()?
James W. MacDonald
jmacdon at uw.edu
Mon Oct 14 16:24:46 CEST 2013
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:
Search by name for an object (‘get’) or zero or more objects
get(x, pos = -1, envir = as.environment(pos), mode = "any",
inherits = TRUE)
mget(x, envir = as.environment(-1), mode = "any", ifnotfound,
inherits = FALSE)
x: For ‘get’, an object name (given as a character string).
For ‘mget’, a character vector of object names.
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:
>>> 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.
>>> Error in .checkKeysAreWellFormed(keys) :
>>> keys must be supplied in a character vector with no NAs
>>>  "character"
>>>  4
>>>> get(symb[], org.Hs.egSYMBOL2EG)
>>>  "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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James W. MacDonald, M.S.
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099
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