Entering edit mode
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
>
