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

[David Winsemius]

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")

?

>
>>
>> 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