diffAnaGetSignificant {DAPAR} | R Documentation |
Returns a MSnSet object with only proteins significant after differential analysis.
diffAnaGetSignificant(obj)
obj |
An object of class |
A MSnSet
Alexia Dorffer
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) limma <- limmaCompleteTest(qData,sTab) fc <- limma$FC[1] pval <- limma$P_Value[1] params <- list(design="OnevsOne", method="limma", th_logFC=0) obj <- diffAnaSave(obj, limma,list(FC=fc, P_Value = pval), params) signif <- diffAnaGetSignificant(obj)