# NOT RUN {
data("alldata_eg")
logdata<-LogTransform(alldata_eg$featuredata)
sampledata<-alldata_eg$sampledata
metabolitedata<-alldata_eg$metabolitedata
imp <- MissingValues(logdata$featuredata,sampledata,metabolitedata,
feature.cutof=0.8, sample.cutoff=0.8, method="knn")
featuredata<-imp$featuredata
qcmets<-which(metabolitedata[,1]=="IS")
factormat<-model.matrix(~gender +Age , sampledata)
#Linear model fit with ordinary statistics with ruv2
ordFit_ruv2<-LinearModelFit(featuredata=featuredata,
factormat=factormat,
ruv2=TRUE, qcmets=qcmets,
k=2)
#Volcano plot
VolcanoPlot(coef=ordFit_ruv2$coefficients[,3],
pval=ordFit_ruv2$p.value[,3],
cexlab = 0.8,
interactiveplot = TRUE,
coeflimit = 0.05,
xlab="Coef",
negcontrol= rownames(ordFit_ruv2$coefficients)
[which(metabolitedata[,2]==1)],
poscontrol= c("m74", "m161"),
interactiveonly = TRUE)
# }
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