HTSanalyzeR (version 2.24.0)

viewGSEA: Plot a figure of GSEA results for one gene set

Description

This is a generic function.

When implemented as the S4 method for objects of class GSCA, this function plots a figure of the positions of the gene sets in the ranked gene list and the location of the enrichment score.

To use this function for objects of class GSCA:

viewGSEA(object, gscName, gsName)

Usage

viewGSEA(object, ...)

Arguments

object

an object. When this function is implemented as the S4 method of class GSCA, this argument is an object of class GSCA.

...

other arguments. (see below for the arguments supported by class GSCA)

Details

We suggest to print the names of top significant gene sets using the function getTopGeneSets before plotting the GSEA results.

See Also

plotGSEA, gseaPlots

Examples

## Not run: 
# library(org.Dm.eg.db)
# library(KEGG.db)
# ##load sample data
# data("KcViab_GSCA")
# ##print summary of results
# summarize(KcViab_GSCA, what="Result")
# ##print top significant gene sets in GO.BP
# topPWKEGG<-getTopGeneSets(KcViab_GSCA, "GSEA.results", "PW_KEGG", allSig=TRUE)
# ##view a gene set
# viewGSEA(KcViab_GSCA, "PW_KEGG", topPWKEGG[["PW_KEGG"]][1])
# ## End(Not run)