| contrasts.varFit {missMethyl} | R Documentation |
Compute estimated coefficients, standard errors and LogVarRatios for a given set of contrasts.
contrasts.varFit(fit, contrasts = NULL)
fit |
List containing a linear model fit produced by |
contrasts |
Numeric matrix with rows corresponding to coefficients in
|
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.
A list object of the same class as fit.
Belinda Phipson
varFit, contrasts.fit, makeContrasts
# 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")
# Fit linear model for differential variability
vfit<-varFit(y,design)
# 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)