diffAnaVolcanoplot {DAPAR} | R Documentation

## Volcanoplot of the differential analysis

### Description

Plots a volcanoplot after the differential analysis. Typically, the log of Fold Change is represented on the X-axis and the log10 of the p-value is drawn on the Y-axis. When the `threshold_pVal` and the `threshold_logFC` are set, two lines are drawn respectively on the y-axis and the X-axis to visually distinguish between differential and non differential data.

### Usage

    diffAnaVolcanoplot(
      logFC = NULL,
      pVal = NULL,
      threshold_pVal = 1e-60,
      threshold_logFC = 0,
      conditions = NULL,
      colors = NULL
    )

### Arguments

`logFC` | A vector of the log(fold change) values of the differential analysis.
`pVal` | A vector of the p-value values returned by the differential analysis.
`threshold_pVal` | A floating number which represents the p-value that separates differential and non-differential data.
`threshold_logFC` | A floating number which represents the log of the Fold Change that separates differential and non-differential data.
`conditions` | A list of the names of condition 1 and 2 used for the differential analysis.
`colors` | xxx

### Value

A volcanoplot

### Author(s)

Florence Combes, Samuel Wieczorek

### Examples

    utils::data(Exp1_R25_pept, package='DAPARdata')
    obj <- Exp1_R25_pept[1:1000]
    keepThat <- mvFilterGetIndices(obj, condition='WholeMatrix', threshold=ncol(obj))
    obj <- mvFilterFromIndices(obj, keepThat)
    qData <- Biobase::exprs(obj)
    sTab <- Biobase::pData(obj)
    limma <- limmaCompleteTest(qData,sTab)
    diffAnaVolcanoplot(limma$logFC[,1], limma$P_Value[,1])

[Package DAPAR version 1.22.9 Index]