diffAnaSave {DAPAR} | R Documentation

## Returns a `MSnSet` object with the results of the differential analysis performed with `limma` package.

### Description

This method returns a class `MSnSet` object with the results of differential analysis.

### Usage

    diffAnaSave(obj, allComp, data = NULL, l.params)

### Arguments

`obj` | An object of class `MSnSet`.
`allComp` | A list of two items which is the result of the function wrapper.limmaCompleteTest or xxxx
`data` | The result of the differential analysis processed by `limmaCompleteTest`
`l.params` | A list of parameters: comp The name of the comparison th_pVal A float that indicates the threshold on p-value choosen to discriminate differential proteins. fdr The FDR based on the values of threshold_pVal and threshold_logFC calibMethod The calibration method used to compute the calibration plot design xxxxxx th_logFC xxxx

### Value

A MSnSet

### Author(s)

Alexia Dorffer, Samuel Wieczorek

### 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)
    allComp <- limmaCompleteTest(qData,sTab)
    data <- list(FC=allComp$FC[1], P_Value = allComp$P_Value[1])
    params <- list(design="OnevsOne", method="limma", th_logFC=0)
    diffAnaSave(obj, allComp, data, params)

[Package DAPAR version 1.12.11 Index]