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, data, method = "limma", condition1, condition2, threshold_pVal = 1e-60, threshold_logFC = 0, fdr = 0, calibrationMethod = "pounds")
obj |
An object of class |
data |
The result of the differential analysis processed
by |
method |
The method used for differential analysis. Available choices are : "limma", "Welch" |
condition1 |
A vector containing the names (some values of the slot
"Label" of |
condition2 |
A vector containing the names (some values of the slot
"Label" of |
threshold_pVal |
A float that indicates the threshold on p-value choosen to discriminate differential proteins. |
threshold_logFC |
A float that indicates the threshold on log(Fold Change) to discriminatedifferential proteins. |
fdr |
The FDR based on the values of threshold_pVal and threshold_logFC |
calibrationMethod |
The calibration method used to compute the calibration plot |
A MSnSet
Alexia Dorffer, Samuel Wieczorek
require(DAPARdata) data(Exp1_R25_pept) condition1 <- '25fmol' condition2 <- '10fmol' limma <- wrapper.diffAnaLimma(Exp1_R25_pept[1:1000], condition1, condition2) obj <- diffAnaSave(Exp1_R25_pept[1:1000], limma, "limma", condition1, condition2)