summary
method for class 'TcGSA
'
Value
The function summary.TcGSA returns a list with the following components (list elements):
time_func
the chosen form for the time trend.separateSubjects
a logical flag indicating whether gene sets tested for discriminating among patients, or for time trends over time.ntg
the number of treatment groups.ngs
the number of tested gene sets.nsignif
the number of significant gene sets at a 5% FDR (using the default Benjamini & Yekutieli step-up procedure).
Examples
if(interactive()){
data(data_simu_TcGSA)
tcgsa_sim_1grp <- TcGSA.LR(expr=expr_1grp, gmt=gmt_sim, design=design,
subject_name="Patient_ID", time_name="TimePoint",
time_func="linear", crossedRandom=FALSE)
summary(tcgsa_sim_1grp)
tcgsa_sim_2grp <- TcGSA.LR(expr=expr_2grp, gmt=gmt_sim, design=design,
subject_name="Patient_ID", time_name="TimePoint",
time_func="linear", crossedRandom=FALSE,
group_name="group.var")
summary(tcgsa_sim_2grp)
}