diffAnaVolcanoplot: Volcanoplot of the differential analysis

In prostarproteomics/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

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(100)]
level <- 'protein'
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), 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])

prostarproteomics/DAPAR documentation built on March 28, 2024, 4:44 a.m.