data_simu_TcGSA: Simulated Data for TcGSA

In borishejblum/TcGSA: Time-Course Gene Set Analysis

Simulated Data for TcGSA

Description

Simulated data for 5 gene sets of 50 genes each. Gene expression is simulated at 5 time points for 10 patients.

Usage

data(data_simu_TcGSA)

Details

In expr_1grp all patients belong to the same unique treatment group. The first 2 gene sets are simulated under the null hypothesis. The gene sets 3 and 4 are simulated under the alternative hypothesis that there is a significant homogeneous time trend within the gene set. The gene set 5 is simulated under the alternative hypothesis that there are significant heterogeneous time trends within the gene set.

In expr_2grp all patients belong to 2 treatment groups. The 5 first patients belong to the treatment group 'T', The 5 other patients belong to the treatment group 'C'. The first 2 gene sets are simulated under the null hypothesis that there is no difference in the time trend between the 2 treatment groups. The gene sets 3 and 4 are simulated under the alternative hypothesis that there are significantly different homogeneous time trends within the gene set between the 2 treatment groups. The gene set 5 is simulated under the alternative hypothesis that there are significantly different heterogeneous time trends between the 2 treatment groups within the gene set.

Value

expr_1grp	See Details.
expr_2grp	See Details.
design	a data frame with 5 variables: Patient_ID: a factor that contains the patient ID. TimePoint: a numeric vector or a factor that contains the time points at which gene expression was measured. sample_name: a character vector with the names of the sample (corresponding to the names of the columns of expr_1grp and of expr_2grp). group.var: a factor that indicates to which of the 2 treatment groups each sample belongs to. Group_paired_ID a random paired identifier for paired couples (one in each of the 2 treatment groups) of patients.
gmt_sim	a gmt object containing the gene sets definition. See GSA.read.gmt and GMT definition on www.broadinstitute.org.

Author(s)

Boris P. Hejblum

Source

This is simulated data.

See Also

TcGSA.LR

Examples

data(data_simu_TcGSA)
summary(expr_1grp)
summary(design)
gmt_sim

borishejblum/TcGSA documentation built on March 24, 2022, 2:21 a.m.