ReplotGSEA: Replot output from the desktop tool javaGSEA.

In PeeperLab/Rtoolbox: Toolbox with R scripts

Description

Creates GSEA plots from the output of the desktop tool javaGSEA.

Usage

replotGSEA(path, gene.set, class.name, metric.range, enrichment.score.range)

Arguments

path	path to the output folder of javaGSEA
gene.set	name of the gene set to be plotted. Approximate matching is used to determine the right gene set.
class.name	name of the variable to which gene expression has been matched (i.e., the description of the variable that is specified in the .cls file or that is used to pre-rank the data; example: "drug treatment").
metric.range	optional; the range of the ranking metric that is plotted. Defaults to [min(ranking metric), max(ranking metric)]
enrichment.score.range	optional; the range of the enrichment score that is plotted. Defaults to [min(enrichment score), max(enrichment score)]

Details

replotGSEA will recreate a GSEA plot from the output of the desktop tool javaGSEA.

Author(s)

Thomas Kuilman ([e-mail])

Examples

## Recreate GSEA plot:

## Not run: replotGSEA(path = path, gene.set = "V$AP1_Q2",
                    class.name = "Drug treatment", metric.range = c(-1, 1))
## End(Not run)

PeeperLab/Rtoolbox documentation built on May 8, 2019, 1:28 a.m.