wrapperCalibrationPlot: Performs a calibration plot on an 'MSnSet' object, calling...

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

Performs a calibration plot on an MSnSet object, calling the cp4p package functions.

Description

This function is a wrapper to the calibration.plot method of the cp4p package for use with MSnSet objects.

Usage

wrapperCalibrationPlot(vPVal, pi0Method = "pounds")

Arguments

vPVal	A dataframe that contains quantitative data.
pi0Method	A vector of the conditions (one condition per sample).

Value

A plot

Author(s)

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)
wrapperCalibrationPlot(limma$P_Value[, 1])

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