limmaTopTable2dgeTable: Transform limma::topTable results to a DGEtable

In bedapub/ribiosExpression: Expression Analysis with RibiosExpression

Transform limma::topTable results to a DGEtable

Description

Transform limma::topTable results to a DGEtable

Usage

limmaTopTable2dgeTable(limmaTopTable)

Arguments

limmaTopTable

topTable returned by limma::topTable

Value

A data.frame known as DGEtable which has controlled column names

Examples

example.sd <- 0.3*sqrt(4/rchisq(100,df=4))
example.y <- matrix(rnorm(100*6,sd=example.sd),100,6)
example.y[1:2,4:6] <- example.y[1:2,4:6] + 2
rownames(example.y) <- paste("Gene",1:100)
example.design <- cbind(Grp1=1,Grp2vs1=c(0,0,0,1,1,1))
example.fit <- limma::lmFit(example.y,example.design)
example.fit <- limma::eBayes(example.fit)
example.tt <- limma::topTable(example.fit, coef=2)
example.dt <- limmaTopTable2dgeTable(example.tt)
head(example.dt)

bedapub/ribiosExpression documentation built on Sept. 2, 2023, 4:37 a.m.