diffAnaGetSignificant {DAPAR}R Documentation

Returns a MSnSet object with only proteins significant after differential analysis.

Description

Returns a MSnSet object with only proteins significant after differential analysis.

Usage

diffAnaGetSignificant(obj)

Arguments

obj

An object of class MSnSet.

Value

A MSnSet

Author(s)

Alexia Dorffer

Examples

require(DAPARdata)
data(Exp1_R25_pept)
obj <- Exp1_R25_pept
keepThat <- mvFilterGetIndices(obj, 'wholeMatrix', ncol(obj))
obj <- mvFilterFromIndices(obj, keepThat)
qData <- Biobase::exprs(obj)
sTab <- Biobase::pData(obj)
limma <- limmaCompleteTest(qData,sTab)
fc <- limma$FC[1]
pval <- limma$P_Value[1]
params <- list(design="OnevsOne", method="limma", th_logFC=0)
obj <- diffAnaSave(obj, limma,list(FC=fc, P_Value = pval), params)
signif <- diffAnaGetSignificant(obj)

[Package DAPAR version 1.12.11 Index]