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

Description Usage Arguments Details Value Examples

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.

Usage

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## S4 method for signature 'GSCA'
viewGSEA(object, gscName, gsName)

Arguments

object

A GSCA object.

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.

Value

In the end, this function would draw a GSEA figure for specified gene set.

Examples

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## load a GSCA object(see the examples of analyze GSCA for details)
data(d7_gsca)

## summarize gsca
summarize(d7_gsca)

## print top significant gene sets in GO_MF
topGS_GO_MF <- getTopGeneSets(d7_gsca, "GSEA.results", gscs = "GO_MF", allSig=TRUE)

## view GSEA results for one gene set
## Not run: 
viewGSEA(d7_gsca, "GO_MF", topGS_GO_MF[["GO_MF"]][1])

## End(Not run)

CityUHK-CompBio/HTSanalyzeR2 documentation built on Dec. 11, 2018, 8:06 a.m.