#' cutoff
#'
#' .
#'
#' @param data .
#' @param method .
#' @param stringency .
#' @param Min .
#' @param minparents .
#'
#' @return value
#'
#' @export
cutoff<- function(data,method,stringency,Min,minparents){
requireNamespace("modes", quietly = TRUE)
d.initial<- GoTheDist(data,method=paste(method),Min=Min,minparents=minparents)
q<-quantile(d.initial,c(.05,.25,.5,.75,.95))
if(method=="cosine"){
qq<-match(T,q!=0)
cut<- distandcyto(data, method=paste(method),low.cutoff=q[qq],high.cutoff=Inf,Min=Min,minparents=minparents )
}
else{
cut<- distandcyto(data, method=paste(method),low.cutoff=-Inf,high.cutoff=q[3],Min=Min,minparents=minparents )
}
dist<- cut[,3]
peaks<- amps(dist)$Peaks
sec_peak<- peaks[2,1]
s_t_midpoint<- mean(c(peaks[3,1],peaks[2,1]))
third_peak<-peaks[3,1]
three_four_midpoint<- mean(c(peaks[3,1],peaks[4,1]))
fourth_peak<-peaks[4,1]
if(stringency==2){
return(sec_peak)
}
if(stringency==2.5){
return(s_t_midpoint)
}
if(stringency==3){
return(third_peak)
}
if(stringency==3.5){
return(three_four_midpoint)
}
if(stringency==4){
return(fourth_peak)
}
}
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