[R] Using getSYMBOL, annotate package on a list with empty elements.

[Martin Morgan]

On 02/13/2010 07:17 AM, David Winsemius wrote:
> 
> On Feb 13, 2010, at 10:09 AM, Martin Morgan wrote:
> 
>> On 02/13/2010 06:21 AM, David Winsemius wrote:
>>>
>>> On Feb 13, 2010, at 3:18 AM, Sahil Seth wrote:
>>>
>>>> Hi,
>>>> I have been trying to find a solution to this issue, but have not been
>>>> able
>>>> to so !
>>>> I am trying to use sapply on the function getSYMBOL,
>>>
>>> The annotate package is from BioConductor.
>>>
>>>> an extract from the list is:
>>>>> test.goP[13:14]
>>>> $`GO:0000050`
>>>>     IEA       IEA       IEA       IEA       TAS       TAS       TAS
>>>> IEA
>>>> "5270753" "5720725" "1690128" "4850681"  "110433" "2640544" "4900370"
>>>> "1430280"
>>>>     IEA       NAS       TAS       IEA
>>>> "6110044" "1170615" "6590546" "1690632"
>>>>
>>>> $`GO:0000052`
>>>> [1] NA
>>>>
>>>> goG=sapply(test.goP,getSYMBOL,data="hgu95av2")
>>>
>>> I was a bit surprised to see a data= argument to sapply. That didn't
>>> seem typical but perhaps I am not aware of all the tricks available.
>>
>>> args(sapply)
>> function (X, FUN, ..., simplify = TRUE, USE.NAMES = TRUE)
>>
>> The ... arguments are passed to FUN. Here FUN is getSYMBOL
>>
>>> args(getSYMBOL)
>> function (x, data)
>>
>> so data="hgu95av2" is used in each application of getSYMBOL. This could
>> have been written as
>>
>>  sapply(test.goP, getSYMBOL, "hgu95av2")
>>
>> using positional matching to getSYMBOL's arguments. A 'trick' that is
>> sometimes useful is to use named arguments to force the apply to vary
>> the second (or other) argument, rather than the first.
>>
>>
>>>> error: "Error in .checkKeysAreWellFormed(keys) :
>>>> keys must be supplied in a character vector with no NAs "
>>>> In this the 14th element has missing values, thus getSYMBOL raises
>>>> issues.
>>>
>>> The way this is being displayed makes me think you are processing a list
>>> with named elements. You should use str to determine what test.goP
>>> really is. Then you will have a better idea what functions would be
>>> appropriate. you may want to compose a function to go with the sapply
>>> loop that omots the NA's:
>>>
>>> ?na.omit
>>>
>>> You should also post the results of dput or dump on the test objects you
>>> are working with. That way the list readers can also get access to that
>>> information.
>>>>
>>>> GetSYMBOL has to be given a char array, so a simple solution is
>>>> infact to
>>>> delete the missing elements from the list.
>>>>
>>>> I have been trying to find a solution for it, but in vain:
>>>> tried: completecases(goP), na.omit(goP) and several other things.
>>>>
>>>> Any suggestions please ?
>>
>>
> 
> Would that be:
> 
>  sapply(!is.na(test.goP), getSYMBOL, "hgu95av2")

actually,

  sapply(test.goP[!is.na(test.goP)], getSYMBOL, "hgu95av2")

;).

Martin

> 
> ?
> 
>>
>>>
>>> In addition to the above suggestions ... post on the correct list?
>>
>>  http://bioconductor.org/
>>
>> Martin
>>
>>>
>>>> -- 
> 
> 
>> Phone: (206) 667-2793
> 
> David Winsemius, MD
> Heritage Laboratories
> West Hartford, CT
> 


-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793