R/calcul_e.R

In TTMap: Two-Tier Mapper: a clustering tool based on topological data analysis

calcul_e<-
function(dd5, pvalcutoff = 0.95, tt1,
alpha = 1, S = colnames(tt1$Normal.mat)){
    w <- apply(tt1$Normal.mat[,
    colnames(tt1$Normal.mat)%in%S], 1, mean)
    w2 <- apply(tt1$Normal.mat[,
    colnames(tt1$Normal.mat)%in%S], 1, sd)
    m_f <- apply(tt1$flat.Nmat$mat[rownames(tt1$Normal.mat),
    colnames(tt1$flat.Nmat$mat)%in%S], 1, min)
    m2_f <- apply(tt1$flat.Nmat$mat[rownames(tt1$Normal.mat),
    colnames(tt1$flat.Nmat$mat)%in%S], 1, max)
    ##Calculate p3
    p2 <- lapply(seq_len(length(m_f)), function(i){
        pnorm(m_f[i], w[i], w2[i], lower.tail = TRUE)
    })
    p2 <- unlist(p2)
    p2p <- lapply(seq_len(length(m_f)), function(i){
        pnorm(m_f[i] - alpha, w[i], w2[i], lower.tail = TRUE)})
    p2p <- unlist(p2p)
    p3 <- lapply(seq_len(length(m_f)), function(i){
        pnorm(m2_f[i], w[i], w2[i], lower.tail = TRUE)})
    p4 <- lapply(seq_len(length(m_f)), function(i){
        pnorm(m_f[i], w[i], w2[i], lower.tail = TRUE)})
    p3 <- unlist(p3)
    p4 <- unlist(p4)
    p3 <- p3 - p4
    p1 <- lapply(seq_len(length(m_f)), function(i){ 
        pnorm(m2_f[i], w[i], w2[i], lower.tail = FALSE)})
    p1p <- lapply(seq_len(length(m_f)), function(i){
        pnorm(m2_f[i] + alpha, w[i], 
        w2[i], lower.tail = FALSE)})
    p1 <- unlist(p1)
    p1p <- unlist(p1p)
    a3 <- 2 * (((p3 + p1) * p2p) + 
    ((p3 + p2) * p1p) - (p1p * p2p))
    sl <- lapply(seq_len(length(as.vector(dd5[upper.tri(dd5)]))),
    function(i){ 
        ele <- as.vector(dd5[upper.tri(dd5)])[i]
        s <- ppois(ele * length(m_f), sum(a3), 
        lower.tail = TRUE, log.p = FALSE)
        ifelse(s < pvalcutoff, ele, 0)
    })
    s <- max(unlist(sl))
    if(s <= 0){
        sl <- lapply(seq_len(length(as.vector(dd5[upper.tri(dd5)]))),
        function(i){ 
            ele <- as.vector(dd5[upper.tri(dd5)])[i]
    #s <- pnorm(ele*length(m_f), mean = sum(a3,na.rm=TRUE), 
    #sd = sqrt(sum(a3*(1-a3),na.rm=TRUE)), lower.tail = TRUE)
            s <- ppois(ele * length(m_f), sum(a3), 
            lower.tail = TRUE, log.p = FALSE)
            ifelse(s < 1-.Machine$double.neg.eps, ele, 0)})
        s <- max(unlist(sl))}
    return(s)
}