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, th_pval = 0, th_logFC = 0)

### 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`
`th_pval` | xxx
`th_logFC` | xxx

### Value

A MSnSet

### Author(s)

Alexia Dorffer, Samuel Wieczorek

### Examples

    utils::data(Exp1_R25_prot, package='DAPARdata')
    obj <- Exp1_R25_prot[1:1000]
    level <- obj@experimentData@other$typeOfData
    metacell.mask <- match.metacell(GetMetacell(obj), 'missing', level)
    indices <- GetIndices_WholeMatrix(metacell.mask, op='>=', th=1)
    obj <- MetaCellFiltering(obj, indices, cmd='delete')
    qData <- Biobase::exprs(obj$new)
    sTab <- Biobase::pData(obj$new)
    allComp <- limmaCompleteTest(qData,sTab)
    data <- list(logFC=allComp$logFC[1], P_Value = allComp$P_Value[1])
    diffAnaSave(obj$new, allComp, data)

[Package DAPAR version 1.24.8 Index]