l.clust: a function to cluster a set of motifs by levenshtein...

In muhligs/Regmex: Motif discovery in ranked lists of sequences

Usage

l.clust(set, k, plot = TRUE, method = "average")

Arguments

set
k
plot
method

Examples

##---- Should be DIRECTLY executable !! ----
##-- ==>  Define data, use random,
##--	or do  help(data=index)  for the standard data sets.

## The function is currently defined as
function (set, k, plot = TRUE, method = "average") 
{
    d <- adist(set)
    rownames(d) <- set
    hc <- hclust(as.dist(d), method = method)
    c.ex <- ifelse(length(set) < 70, 30/length(set), 40/length(set))
    if (plot == TRUE) 
        plot(hc, xlab = "motifs", cex = c.ex)
    rect.hclust(hc, k = k)
    return(data.frame(cutree(hc, k = k)))
  }

muhligs/Regmex documentation built on Sept. 5, 2020, 1:11 a.m.