# This function returns an object of class "dist"
sim2dist <- function(mx)
as.dist(sqrt(outer(diag(mx), diag(mx), "+") - 2*mx))
# from similarity to distance matrix
d.mx = as.matrix(d.mx)
d.mx = sim2dist(d.mx)
# The distance matrix can be used to visualize
# hierarchical clustering results as dendrograms
hc = hclust(d.mx)
plot(hc)See Multivariate Analysis (Probability and Mathematical Statistics)
for the statistical theory.
Thank you a lot!
RispondiElimina(I suppose s.mx should be d.mx)
Dotoma
You're right! Fixed! Thank you!
RispondiEliminawhich page/section is the theory? Thank you!
RispondiEliminaDear Jianhua, this post was written long time ago (2007) and unfortunately I don't have access to that book anymore...
RispondiEliminaThe RFLPtools package seems to present a similar function, take a loot at http://rgm3.lab.nig.ac.jp/RGM/r_function?p=RFLPtools&f=sim2dist as a starting point. HIH!