R/ttmap_sgn_genes_inter.R

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

ttmap_sgn_genes_inter <-
function(q, ttmap_part1_hda, alpha = 0){
    A <- ttmap_part1_hda$Dc.Dmat[
    ,colnames(ttmap_part1_hda$Dc.Dmat) %in% q]
    if(length(q) > 1){
        A <- A[rowSums(abs(A)) > 0, ]
        A[A == 0]<-NA
        A <- as.matrix(A)
        w <- apply(abs(A), 1, max, na.rm=TRUE)
        w2 <- apply(A, 1, max, na.rm=TRUE)
        w3 <- apply(A, 1, min, na.rm=TRUE)
        w2 <- sign(w2 * w3)
    }
    else{
        A <- as.matrix(A)
        rownames(A) <- rownames(ttmap_part1_hda$Dc.Dmat)
        w <- abs(A[A != 0, ])
        w2 <- sign(w)
    }
    select2 <- names(w2[w2[] == 1])
    #we just don't want those which are different
    select <- names(w[w[] > alpha])
    # we will only consider those which are different than alpha
    s <- intersect(select, select2)
    if(length(s) == 1){
        A <- as.matrix(A[s, ])
        rownames(A) <- s
    }
    else{A <- A[s, ]}
    return(A)}