Nothing
"cond.test"<-function(data, groups=NULL, kappa = NULL, biasCorrect = TRUE){
# DATE WRITTEN: 4 Ago 2010 LAST REVISED: 22 Ene 2013
# AUTHOR: Sandra Barragan based on the SAS routines written by Miguel A. Fernandez.
# DESCRIPTION:
# data are the unordered estimator
# replic=T means that data have replication => kappa estimated
# kappa is the value of kappa when is known
# REFERENCE: Fernandez, M. A., Rueda, C. and Shyamal, P. (2012).
# Identification of a core set of signature cell cycle genes whose relative order of time to peak expression is conserved across
# species, \emph{Nucl. Acids Res.} \bold{40}, n7: pp 2823--2832. doi:10.1093/nar/gkr1077.
# SEE ALSO: mrl, CIRE.
if(is.vector(data)){data <- cbind(data)}
if(ncol(data) == 1 && missing(kappa)){stop("If data do not have replications, kappa must be known")}
if(is.null(groups)){stop("The order in the null hypothesis must be defined in the argument groups")}
n <- as.vector(table(groups[!apply(data,1,is.na)]))
posi <- prod(factorial(n))
resultCIRE <- CIRE(data, groups, circular=TRUE)
SCE <- resultCIRE$SCE
ordermeans <- unlist(resultCIRE$CIRE)
data1 <- sort(ordermeans)
data2 <- c(data1[2:length(data1)],data1[1])
difference <- ifelse((data1 - data2) == 0, 0, 1)
m <- sum(difference)
q <- length(ordermeans)
if(!is.null(kappa)& SCE!=0){
kap <- kappa
ST <- 2*kap*SCE
pvalue <- pchisq(ST, q-m, lower.tail=FALSE)*(1 - ((posi)/(factorial(q - 1))))
} # end kappa known
if(is.null(kappa)){
Rs<-apply(data,1,mrl)
kappa<-A1inv(mean(Rs))
kap <- kappa
if(biasCorrect == TRUE) {
N<-ncol(data)*nrow(data)
if(kap < 2){
kap<-max(kap-(2/(N*kap)), 0)
}else{
kap<-(((N-1)^3)*kap)/((N^3)+N)
}
}
if(SCE!=0){
ST <- 2*kap*SCE
pvalue <- pf(ST, q-m, q-1, lower.tail=FALSE)*(1 - ((posi)/(factorial(q - 1))))
}
} # end kappa unknown and replications
if(SCE==0){
pvalue<-1
#warning("SCE=0")
}
lexit <- resultCIRE
class(lexit)<-"isocir"
lexit$pvalue <- pvalue
lexit$kappa <- kappa
attr(lexit,"estkappa")<-ifelse(is.null(kappa),"Kappa has been estimated","Kappa was known")
return(lexit)
} # end cond.test
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