I'm using R to perform an hierarchical clustering. As a first approach I used hclust
and performed the following steps:
as.dist
function to transform it in a dist
objecthclust
on the dist
objectHere's the R code:
distm <- read.csv("distMatrix.csv")
d <- as.dist(distm)
hclust(d, "ward")
At this point I would like to do something similar with the function pvclust
; however, I cannot because it's not possible to pass a precomputed dist
object. How can I proceed considering that I'm using a distance not available among those provided by the dist
function of R?
It's not clear to me whether you only have a distance matrix, or you computed it beforehand. In the former case, as already suggested by @Vincent, it would not be too difficult to tweak the R code of pvclust
itself (using fix()
or whatever; I provided some hints on another question on CrossValidated). In the latter case, the authors of pvclust provide an example on how to use a custom distance function, although that means you will have to install their "unofficial version".