[R] clustering problem
Karin Lagesen
karin.lagesen at medisin.uio.no
Wed Feb 20 11:10:30 CET 2008
First I just want to say thanks for all the help I've had from the
list so far..)
I now have what I think is a clustering problem. I have lots of
objects which I have measured a dissimilarity between. Now, this list
only has one entry per pair, so it is not symmetrical.
Example input:
NameA NameB Dist
189_1C2 189_1C1 0
189_1C3 189_1C1 0.017
189_1C3 189_1C2 0.017
189_1C4 189_1C1 0
189_1C4 189_1C2 0
189_1C4 189_1C3 0.017
189_1C5 189_1C1 0.05
189_1C5 189_1C2 0.05
189_1C5 189_1C3 0.067
189_1C5 189_1C4 0.05
189_1C6 189_1C1 0.05
189_1C6 189_1C2 0.05
189_1C6 189_1C3 0.067
189_1C6 189_1C4 0.05
189_1C6 189_1C5 0
The distance measure is 0 if identical, and then increases with
increasing dissimilarity up till 1.
What I would like to get from these data is a hierarchical clustering
graph. In this example I would then group
189_1C2 189_1C1 189_1C4,
189_1C6 189_1C5,
and 189_1C3 off with itself.
The distances between the groups should be the mean distances between
the objects within each group (I think).
I have looked at hclust and it seems like it should be able to do what
I want. However, I am unsure of how to use it to get what I am looking
for.
Thankyou in advance for your help!
Karin
--
Karin Lagesen, PhD student
karin.lagesen at medisin.uio.no
http://folk.uio.no/karinlag
More information about the R-help
mailing list