extractMeanDiff {MSstatsPTM} | R Documentation |
extractMeanDiff
performs significance analysis for detection of
changes in PTM mean abundances between conditions.
extractMeanDiff(data, controls, cases, perProtein = FALSE)
data |
A list of abundance estimates with the following elements:
|
controls |
A string vector of control groups in the comparisons. |
cases |
A string vector of case groups. |
perProtein |
A logical. |
A data frame.
sim <- PTMsimulateExperiment( nGroup=2, nRep=2, nProtein=1, nSite=1, nFeature=5, logAbundance=list( PTM=list(mu=25, delta=c(0, 1), sRep=0.2, sPeak=0.05), PROTEIN=list(mu=25, delta=c(0, 1), sRep=0.2, sPeak=0.05) ) ) summarized <- PTMsummarize(sim) estimates <- PTMestimate(summarized) extractMeanDiff(estimates[["PTM"]], controls="G_1", cases="G_2", FALSE) extractMeanDiff(estimates[["PROTEIN"]], controls="G_1", cases="G_2", TRUE)