diffAnaSave: Returns a 'MSnSet' object with the results of the...

In samWieczorek/DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

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)

samWieczorek/DAPAR documentation built on May 6, 2022, 5:30 p.m.