ES.plot: Enrichment set plot

In jhart99/gseasier: Run the GSEA java pacakage from inside R

Description

Enrichment set plot

Usage

ES.plot(gmt = NULL, cls = NULL, comparison = NULL, geneset = NULL,
  sn.table = NULL, msigdb = NULL)

Arguments

gmt	A gmt formatted gene expression data set
cls	A cls formatted classifier
comparison	Which levels of cls should be compared defaults to levels 1 and 2
geneset	Either a vector of gene identifiers or a geneset name in combination with msigdb parameter
sn.table	(optional) A signal to noise named vector can be used in place of gmt, cls and comparison
msigdb	(optional) A database of signatures

Value

A ggplot2 plot of the GSEA plot

Examples

ES.plot(gender, gender.cls, NULL, sigs$gene[sigs$sig == "chr4q22"])
ES.plot(gender, gender.cls, geneset = sigs$gene[sigs$sig == "chr9p22"])
ES.plot(gender, gender.cls, geneset = "chr9p22", msigdb = sigs)

jhart99/gseasier documentation built on May 20, 2019, 8:31 a.m.