sGBJ {sGBJ}

Compute the sGBJ statistic and its p-value quantifying a gene set expression association with survival

Description

This function is the main function of the sGBJ package to perform Gene Set Analysis in the context of time-to-event outcome.

Usage

sGBJ(surv, factor_matrix, covariates = NULL, nperm = 300)

Arguments

surv

a Surv object of length n

factor_matrix

a n x p data.frame of the expression for the particular gene set of interest being tested

covariates

a n x l matrix of the covariates to adjust upon. Default is NULL

nperm

number of permutations performed to estimate the epsilon matrix. Default is 300.

Value

The sGBJ statistic and its associated p-value associated

Examples

n <- 100
surv_data <- data.frame(Time = runif(n = n, min = 0, max = 100),
                        event = rbinom(n = n, size = 1, prob = 0.5))
surv <- survival::Surv(time = surv_data$Time, event = surv_data$event)

factor_matrix <- data.frame(P1 = rnorm(n = n),
                             P2 = rnorm(n = n))

sGBJ::sGBJ(surv,factor_matrix, nperm = 2)