diffAnaSave {DAPAR} | R Documentation |
MSnSet
object with the results of
the differential analysis performed with limma
package.This method returns a class MSnSet
object with the results
of differential analysis.
diffAnaSave(obj, allComp, data = NULL, l.params)
obj |
An object of class |
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 |
l.params |
A list of parameters: comp The name of the comparison th_pVal A float that indicates the threshold on p-value choosen to discriminate differential proteins. fdr The FDR based on the values of threshold_pVal and threshold_logFC calibMethod The calibration method used to compute the calibration plot design xxxxxx th_logFC xxxx |
A MSnSet
Alexia Dorffer, Samuel Wieczorek
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(FC=allComp$FC[1], P_Value = allComp$P_Value[1]) params <- list(design="OnevsOne", method="limma", th_logFC=0) diffAnaSave(obj, allComp, data, params)