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]