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_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$P_Value[1])
    obj$new <- diffAnaSave(obj$new, allComp, data)
    signif <- diffAnaGetSignificant(obj$new)

[Package DAPAR version 1.24.8 Index]