function_limma: use limma function to get pvalue

In Caleb-Huo/AWFisher: An R package for fast computing for adaptively weighted fisher's method

use limma function to get pvalue

Description

use limma function to get pvalue

Usage

function_limma(astudy)

Arguments

astudy

A list contains a data matrix and a vector of group label

Details

use limma function to get pvalue

Value

A list of pvalue and effect size

Author(s)

Zhiguang Huo

Examples

N0 = 10
G <- 1000
GDEp <- 50
GDEn <- 50

set.seed(15213)

astudy <- matrix(rnorm(N0*2*G),nrow=G,ncol=N0*2)
ControlLabel <- 1:N0
caseLabel <- (N0 + 1):(2*N0)

astudy[1:GDEp,caseLabel] <- astudy[1:GDEp,caseLabel] + 2
astudy[1:GDEp + GDEn,caseLabel] <- astudy[1:GDEp,caseLabel] - 2

alabel <- c(rep(0,length(ControlLabel)),rep(1,length(caseLabel)))
Study <- list(data=astudy, label=alabel)

result <- function_limma(Study)
fdr <- p.adjust(result$pvalue)
sum(fdr<=0.05)

Caleb-Huo/AWFisher documentation built on June 16, 2022, 5:48 p.m.