diffAnaSave: Returns a 'MSnSet' object with the results of the...
In DAPAR: Tools for the Differential Analysis of Proteins Abundance with R

Description Usage Arguments Value Author(s) Examples

This method returns a class MSnSet object with the results of differential analysis.

1	diffAnaSave(obj, allComp, data = NULL, th_pval = 0, th_logFC = 0)

`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

A MSnSet

Alexia Dorffer, Samuel Wieczorek

utils::data(Exp1_R25_pept, package='DAPARdata')
obj <- Exp1_R25_pept
keepThat <- mvFilterGetIndices(obj, condition='WholeMatrix', threshold=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)