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

In HTSanalyzeR: Gene set over-representation, enrichment and network analyses for high-throughput screens

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)

gscName:

a single character value specifying the name of the gene set collection where the gene set is

gsName:

a single character value specifying the name of the gene set to be plotted

Details

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

Author(s)

Xin Wang [e-mail]

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)

HTSanalyzeR documentation built on Oct. 31, 2019, 7:10 a.m.