diffAnaVolcanoplot: Volcanoplot of the differential analysis
In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description Usage Arguments Value Author(s) Examples

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.

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

`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

A volcanoplot

Florence Combes, Samuel Wieczorek

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])