fit.edger: edgeR wrapper

In floatofmath/bt88.03.704: floats MSI utility function

edgeR wrapper

Description

Wrapper script that fits an edgeR model and does linear contrast tests.

Usage

fit.edger(data, MM, CM, ...)

Arguments

data	a DGEList object
MM	a model matrix
CM	a contrast matrix if NULL no contrasts will be fit
...	additional parameters passed to glmLRT

Value

a DGELRT object

Author(s)

Florian Klinglmueller

Examples

## setting up some random data
data <- matrix(rpois(600,200),ncol=6)
dge <- DGEList(counts=data)
dge <- estimateDisp(dge)

## a design matrix
design <- data.frame('Treatment' = factor(rep(0:1,each=3)))
mm <- model.matrix(~0+Treatment,design)

## a contrast matrix
colnames(mm) <- c('control','treatment')
cm <- makeContrasts('control-treatment',levels=mm)

## fit and test
out <- fit.edger(dge,mm,cm)

myTopTags(out,3)

floatofmath/bt88.03.704 documentation built on March 25, 2022, 12:28 p.m.