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

    utils::data(Exp1_R25_pept, package='DAPARdata')
    obj <- Exp1_R25_pept
    keepThat <- mvFilterGetIndices(obj, 'wholeMatrix', 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)

[Package DAPAR version 1.20.3 Index]