[BioC] Adding to GeneSetCollection object from function

[Martin Morgan]

On 03/12/2011 02:14 AM, Iain Gallagher wrote:
> oops, just correcting a typo in the code!
> 
> library(GSEABase)
> 
> testList <- list('hsa-mir-451'=c('SATB2', 'MECP2', 'CTNNBIP1'), 'hsa-mir-452'=c('SATB2', 'MEIS2', 'PRDM16'), 'hsa-mir-453'=c('SATB2', 'SNAI1', 'MECP2'))
> 
> geneSetFunc <- function(listIn)
>     {
>     l <- length(listIn)
>     setNames <- names(listIn)
> 
> 
>     for (i in 1:l) {
>     gsTest <- GeneSet(unique(listIn[[i]]), geneIdType=SymbolIdentifier(), setName = setNames[i])
>     }
>     
>     return(gsTest)
> }

Hi Iain --

I created a list of GeneSets from your named list using Map (which is
like mapply). Then I made the list of sets into a GeneSetCollection

geneSetFunc <- function(listIn)
{
    sets <- Map(GeneSet, listIn, setName=names(listIn),
                MoreArgs=list(geneIdType=SymbolIdentifier()))
    GeneSetCollection(sets)
}

Hope that helps,

Martin

> 
> test <- geneSetFunc(testList)
> 
> thanks
> 
> i
> 
> --- On Fri, 11/3/11, Iain Gallagher <iaingallagher at btopenworld.com> wrote:
> 
>> From: Iain Gallagher <iaingallagher at btopenworld.com>
>> Subject: [BioC] Adding to GeneSetCollection object from function
>> To: "bioconductor" <bioconductor at stat.math.ethz.ch>
>> Date: Friday, 11 March, 2011, 21:36
>> Hello list,
>>
>> I have written a small function to create GeneSets from a
>> list object. As each GeneSet is generated I would like to
>> add them to a GeneSetCollection object.
>>
>> How do I do this?
>>
>> #toy code
>> library(GSEABase)
>>
>> testList <- list('hsa-mir-451'=c('SATB2', 'MECP2',
>> 'CTNNBIP1'), 'hsa-mir-452'=c('SATB2', 'MEIS2', 'PRDM16'),
>> 'hsa-mir-453'=c('SATB2', 'SNAI1', 'MECP2'))
>>
>> geneSetFunc <- function(listIn)
>>     {
>>     l <- length(listIn)
>>     setNames <- names(listIn)
>>     for (i in 1:l) {
>>     gsTest <- GeneSet(unique(listIn[[i]]),
>> geneIdType=SymbolIdentifier(), setName = names[i])
>>
>>
>>     }
>>
>>     return(gsTest)
>> }
>>
>> test <- geneSetFunc(testList)
>>
>> test2 <- GeneSetCollection(test)
>>
>> As it stands only the last GeneSet out makes the collection
>> & as each output arrives in the collection it overwrites
>> the previous.
>>
>> Thanks for any help / pointers.
>>
>> best
>>
>> i
>>
>>> sessionInfo()
>> R version 2.12.2 (2011-02-25)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>> locale:
>>  [1] LC_CTYPE=en_GB.utf8   
>>    LC_NUMERIC=C       
>>      
>>  [3] LC_TIME=en_GB.utf8       
>> LC_COLLATE=en_GB.utf8    
>>  [5] LC_MONETARY=C         
>>    LC_MESSAGES=en_GB.utf8   
>>  [7] LC_PAPER=en_GB.utf8   
>>    LC_NAME=C       
>>         
>>  [9] LC_ADDRESS=C           
>>   LC_TELEPHONE=C       
>>    
>> [11] LC_MEASUREMENT=en_GB.utf8 LC_IDENTIFICATION=C 
>>     
>>
>> attached base packages:
>> [1] stats     graphics  grDevices
>> utils     datasets 
>> methods   base     
>>
>> other attached packages:
>> [1] GSEABase_1.12.1      graph_1.28.0 
>>        annotate_1.28.0 
>>    
>> [4] AnnotationDbi_1.12.0 Biobase_2.10.0     
>>
>>
>> loaded via a namespace (and not attached):
>> [1] DBI_0.2-5     RSQLite_0.9-4
>> tools_2.12.2  XML_3.2-0 
>>    xtable_1.5-6 
>>>
>>
>>
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>>
> 
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