viewGSEA {HTSanalyzeR} | R Documentation

## 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`)

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 xw264@cam.ac.uk

### 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)

[Package HTSanalyzeR version 2.32.0 Index]