[BioC] Adding to GeneSetCollection object from function

[Iain Gallagher]

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)
}

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 
> > 
> 
> 
> _______________________________________________
> Bioconductor mailing list
> Bioconductor at r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
>