Nothing
highTtest <- function(dataSet1,
dataSet2,
gammas,
compare="BOTH",
cSequence = NULL,
tSequence = NULL){
compare <- toupper(compare)
if("BOTH" %in% compare) compare <- c("BH","ST")
if(!all(compare %in% c("BH","ST","NONE"))) {
stop("method specified is not available")
}
if(is.data.frame(dataSet1)){
dataSet1 <- data.matrix(dataSet1)
} else if(!is.matrix(dataSet1)){
dataSet1 <- matrix(dataSet1,nrow=1)
}
if(is.data.frame(dataSet2)){
dataSet2 <- data.matrix(dataSet2)
} else if(!is.matrix(dataSet2)){
dataSet2 <- matrix(dataSet2,nrow=1)
}
if(nrow(dataSet2) != nrow(dataSet1)){
stop("data sets must have same # of observations")
}
n1 <- ncol(dataSet1)
n2 <- ncol(dataSet2)
Tstar <- tStatistic(data1 = dataSet1,
data2 = dataSet2)
p_value <- Tstar$pv
po <- order(p_value)
p_value <- p_value[po]
rm(dataSet1, dataSet2)
tmp <- CaoKosorok(Tstar = Tstar$statistic,
gammas = gammas,
cSequence = cSequence,
tSequence = tSequence)
indicator.ck <- tmp$ind
pi1 <- tmp$pi1
if("BH" %in% compare){
indicator.bh <- BenjaminiHochberg(alphas = gammas, p_value = p_value)
indicator.bh[po,] <- indicator.bh
} else {
indicator.bh <- NULL
}
if("ST" %in% compare){
indicator.st <- StoreyTibshirani(alphas = gammas, p_value = p_value)
indicator.st[po,] <- indicator.st
} else {
indicator.st <- NULL
}
p_value[po] <- p_value
HCO <- new("highTtest",
CK = indicator.ck,
pi1 = pi1,
pvalue = p_value,
BH = indicator.bh,
ST = indicator.st,
gammas = gammas)
return(HCO)
}
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