deVolcano: Draw volcano plot of differential expression results

In calebclass/NanoTube: An Easy Pipeline for NanoString nCounter Data Analysis

Draw volcano plot of differential expression results

Description

Draw a volcano plot for results of a differential expression analysis by limma.

Usage

deVolcano(limmaResults, plotContrast = NULL, y.var = c("p.value", "q.value"))

Arguments

limmaResults	Result from runLimmaAnalysis.
plotContrast	Contrast to select for volcano plot. Should be one of the columns in the limma coefficients matrix (for example, a sample group that was compared against the base group, or one of the contrasts in the design matrix). If NULL (default), will plot the first non-Intercept column from the limma coefficients matrix.
y.var	The variable to plot for the y axis, either "p.value" or "q.value" (the false discovery adjusted p-value)

Value

A volcano plot using ggplot2

Examples

data(ExampleResults) # Results from runLimmaAnalysis

deVolcano(ExampleResults, plotContrast = "Autoimmune.retinopathy")

calebclass/NanoTube documentation built on Nov. 21, 2023, 12:31 p.m.