plotreact: rnareactplot function

In pcheng84/TCGAbrowser: Explores and Analyzses TCGA Data

Description

Uses ReactomePA to find enriched pathways from the RNAseq differential gene analysis

Usage

plotreact(react, deg, graph, n)

Arguments

react	data frame generated by rnareact function
deg	data frame generated by rnadeg function
graph	character(1) type of graph to plot, (dot, map, cnet)
n	numeric(1) number of pathways to plot

Value

dotplot or enrichment pathway or cnetmap of Reactome gene sets

Examples

data(skcm)
gene <- "SOX10"
sox10.pat <- rnasubset(pat, rna, gene, 10)
sox10.deg <- rnadeg(sox10.pat, rna)
sox10.react <- rnareact(sox10.deg)
plotreact(sox10.react, sox10.deg, "dot", 15)
plotreact(sox10.react, sox10.deg, "map", 15)
plotreact(sox10.react, sox10.deg, "cnet", 5)

pcheng84/TCGAbrowser documentation built on Sept. 7, 2021, 8:28 p.m.