Question: Using GeneSetCollection objects of GSEABase in piano package
0
gravatar for Lluís Revilla Sancho
2.4 years ago by
European Union
Lluís Revilla Sancho480 wrote:

I am interested in some function of the piano package. I have read the vignette and the help page, and I assumed that the GSC class needed to use runGSA was the GeneSetCollection provided by the GSEABase package of the project.

However when I read in detail the function and compare with the GeneSetCollection object they aren't the same. I have some GeneSetCollections I was using to perform GSA with GSVA, limma ...

Is there a function or method to convert the GeneSetCollection to the GSC objects needed for piano? The only workaround would be to save in gmt format the GeneSetCollection and then load it again:

toGMT(myGeneSetCollection, "myGSC.gmt")
GSCformat <- loadGSC("myGSC.gmt")

I can understand that some GSA test require the data in other format than GeneSetCollection, but couldn't that transformation be done internally? It would be easier to integrate with existing GSEA packages and tools in Bioconductor.

gseabase piano • 389 views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Lluís Revilla Sancho480
1

Hi, thanks for pointing this out. I will aim at including support for the GeneSetCollection class in the next piano update, either directly in runGSA or perhaps by a run through loadGSC.

ADD REPLYlink written 2.4 years ago by Leif Väremo70
Answer: Using GeneSetCollection objects of GSEABase in piano package
1
gravatar for Lluís Revilla Sancho
2.4 years ago by
European Union
Lluís Revilla Sancho480 wrote:

I found another workaround, to convert GeneSetCollection to GSC

GeneSetCollection2GSC <- function(gsc, addInfo = "none") {
  GSC <- list("gsc" = geneIds(gsc), "addInfo" = addInfo)
  class(GSC) <- "GSC"
  return(GSC)
}
myGSC <- geneSetCollection2GSC(myGeneSetCollection)
myGSC

 

ADD COMMENTlink written 2.4 years ago by Lluís Revilla Sancho480
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