How to convert a symmetric matrix into "dist" object?
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 32 2 3 3 2 4 4 1 3Make sure that the values in your matrix are dissimilarity, or distance metrics rather than similarity scores.