# NOT RUN {
# This example shows how to implement the method using LPS RFI data.
data(dat)
data(design)
data(covset)
Subject <- covset$ear
Time <- covset$time
Nboot <- 2 # for real data analysis, use Nboot at least 100
ncores <- 1 # for real data analysis and if the computer allows, increase ncores to save time
print.progress <- FALSE
saveboot <- FALSE
counts <- dat[1:3,]
C.matrix <- list()
# test for Line main effect
C.matrix[[1]] <- limma::makeContrasts(line2, levels = design)
# test for Time main effect
C.matrix[[2]] <- limma::makeContrasts(time2, time6, time24, levels = design)
names(C.matrix) <- c("line2", "time")
TCout <- rmRNAseq:::TC_CAR1(counts, design, Subject, Time, C.matrix,
Nboot, ncores, print.progress, saveboot)
names(TCout)
TCout$pqvalue$pv
TCout$pqvalue$qv
# }
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