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)