deVolcano {NanoTube} | R Documentation

## 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")

[Package NanoTube version 1.0.0 Index]