contrasts.varFit: Compute contrasts for a varFit object.

In Oshlack/missMethyl: Analysing Illumina HumanMethylation BeadChip Data

Compute contrasts for a varFit object.

Description

Compute estimated coefficients, standard errors and LogVarRatios for a given set of contrasts.

Usage

contrasts.varFit(fit, contrasts = NULL)

Arguments

fit	List containing a linear model fit produced by varFit. The fit object should be of class MArrayLM.
contrasts	Numeric matrix with rows corresponding to coefficients in fit and columns containing contrasts.

Details

This function calls the contrasts.fit function in limma to compute coefficients and standard errors for the specified contrasts corresponding to a linear model fit obtained from the varFit function. LogVarRatios are also computed in terms of the contrasts. A contrasts matrix can be computed using the makeContrasts function.

Value

A list object of the same class as fit.

Author(s)

Belinda Phipson

See Also

varFit, contrasts.fit, makeContrasts

Examples

# Randomly generate data for a 3 group problem with 100 CpG sites and 4 
# arrays in each group. 

library(limma)

y<-matrix(rnorm(1200),ncol=12)

group<-factor(rep(c(1,2,3),each=4))
design<-model.matrix(~0+group)
colnames(design)<-c("grp1","grp2","grp3")
design

# Fit linear model for differential variability
# Please always specify the coef parameter in the call to varFit
vfit<-varFit(y,design,coef=c(1,2,3))

# Specify contrasts
contr<-makeContrasts(grp2-grp1,grp3-grp1,grp3-grp2,levels=colnames(design))

# Compute contrasts from fit object
vfit.contr<-contrasts.varFit(vfit,contrasts=contr)

summary(decideTests(vfit.contr))

# Look at top table of results for first contrast
topVar(vfit.contr,coef=1)

Oshlack/missMethyl documentation built on March 26, 2023, 1:50 p.m.