viewGSEA {HTSanalyzeR} | R Documentation |
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)
viewGSEA(object, ...)
object |
an object. When this function is implemented as the S4 method of class
|
... |
other arguments. (see below for the arguments supported by class |
a single character value specifying the name of the gene set collection where the gene set is
a single character value specifying the name of the gene set to be plotted
We suggest to print the names of top significant gene sets using the
function getTopGeneSets
before
plotting the GSEA results.
Xin Wang xw264@cam.ac.uk
## 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)