diffAnaVolcanoplot: Volcanoplot of the differential analysis

In samWieczorek/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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_prot, package='DAPARdata')
obj <- Exp1_R25_prot[1:1000]
level <- obj@experimentData@other$typeOfData
metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1)
obj <- MetaCellFiltering(obj, indices, cmd='delete')
qData <- Biobase::exprs(obj$new)
sTab <- Biobase::pData(obj$new)
limma <- limmaCompleteTest(qData, sTab)
diffAnaVolcanoplot(limma$logFC[,1], limma$P_Value[,1])

samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.