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

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(logFC=allComp$logFC[1], P_Value = allComp$P_Value[1])
diffAnaSave(obj, allComp, data)

[Package DAPAR version 1.16.4 Index]