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

[David Winsemius]

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.

> 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 ?

In addition to the above suggestions ... post on the correct list?

> --

David Winsemius, MD
Heritage Laboratories
West Hartford, CT