diffAnaSave | 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, th_pval = 0, th_logFC = 0)
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 |
th_pval |
xxx |
th_logFC |
xxx |
A MSnSet
Alexia Dorffer, Samuel Wieczorek
data(Exp1_R25_prot, package="DAPARdata") obj <- Exp1_R25_prot[seq_len(100)] level <- 'protein' 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)
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