diffAnaGetSignificant: Returns a MSnSet object with only proteins significant after...

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

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

utils::data(Exp1_R25_pept, package='DAPARdata')
obj <- Exp1_R25_pept
keepThat <- mvFilterGetIndices(obj, condition='WholeMatrix', threshold=ncol(obj))
obj <- mvFilterFromIndices(obj, keepThat)
qData <- Biobase::exprs(obj)
sTab <- Biobase::pData(obj)
allComp <- limmaCompleteTest(qData,sTab)
data <- list(logFC=allComp$logFC[1], P_Value = allComp$P_Value[1])
obj <- diffAnaSave(obj, allComp, data)
signif <- diffAnaGetSignificant(obj)

DAPAR documentation built on April 11, 2021, 6 p.m.