summary.TcGSA: Summarizing TcGSA

In TcGSA: Time-Course Gene Set Analysis

Summarizing TcGSA

Description

summary method for class 'TcGSA'

Usage

## S3 method for class 'TcGSA'
summary(object, ...)

## S3 method for class 'summary.TcGSA'
print(x, ...)

Arguments

object	an object of class 'TcGSA'.
...	further arguments passed to or from other methods.
x	an object of class 'summary.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).

Author(s)

Boris P. Hejblum

See Also

TcGSA.LR

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)
}

TcGSA documentation built on Aug. 8, 2025, 7:18 p.m.