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

In prostarproteomics/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

data(Exp1_R25_prot, package="DAPARdata")
obj <- Exp1_R25_prot[seq_len(100)]
level <- 'protein'
metacell.mask <- match.metacell(GetMetacell(obj), c("Missing POV", "Missing MEC"), 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)

prostarproteomics/DAPAR documentation built on Oct. 11, 2024, 12:03 p.m.