HTSanalyzeR (version 2.24.0)

gseaPlots: Plot GSEA results for one gene set

Description

This function takes in the output of gseaScores and the named vector of phenotypes, and plots the positions of genes of the gene set in the ranked phenotype vector and the location of the enrichment score.

Usage

gseaPlots(runningScore, enrichmentScore, positions, geneList)

Arguments

runningScore

a single numeric value specifying the enrichment score returned from the function "gseaScores"

enrichmentScore

a numeric vector of running sum scores (only in mode "graph")

positions

a numeric vector specifying positions in the ranked phenotype vector of the genes in the gene set (only in mode "graph")

geneList

a numeric or integer vector of phenotypes in descending or ascending order with elements named by their EntrezIds (no duplicates nor NA values)

References

Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S. & Mesirov, J. P. (2005) Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proc. Natl. Acad. Sci. USA 102, 15545-15550.

See Also

plotGSEA, viewGSEA

Examples

## Not run: 
# library(org.Dm.eg.db)
# library(KEGG.db)
# ##load phenotype vector (see the vignette for details about the
# ##preprocessing of this data set)
# data("KcViab_Data4Enrich")
# DM_KEGG <- KeggGeneSets(species="Dm")
# GSCscores <- gseaScores(geneList=KcViab_Data4Enrich, geneSet=DM_KEGG[[1]],
# exponent=1, mode="graph")
# gseaPlots(runningScore=GSCscores$runningScore, enrichmentScore=
# GSCscores$enrichmentScore, positions=GSCscores$positions,
# geneList=KcViab_Data4Enrich)
# ## End(Not run)