How to convert a symmetric matrix into "dist" object?

distance, matrix, r

Solution

It sounds like you already have a matrix calculated, and want to use that in hclust. Like @shadow said, you can use `as.dist(yourMatrix)` to convert to the dist format.

Given a symmetric table of distances:

> yourMatrix<-matrix(c(1,2,3,4,2,1,2,1,3,2,1,3,4,1,3,1), nrow=4)
     [,1] [,2] [,3] [,4]
[1,]    1    2    3    4
[2,]    2    1    2    1
[3,]    3    2    1    3
[4,]    4    1    3    1
>
>as.dist(yourMatrix)
  1 2 3
2 2    
3 3 2  
4 4 1 3

Make sure that the values in your matrix are dissimilarity, or distance metrics rather than similarity scores.

Problem

I want to use `hclust` to cluster a data. But I don't want to use "dist()" to generate the dist object. Then I found out that I cannot pass a symmetric matrix as distance matrix into `hclust`. How to convert a symetric matrix into "dist" object?

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