[Biodevelopers] Running hierarchical single linkage clustering on R

[Dan Bolser]

Shalini Sridhar wrote:
> Hi
> 
> Currently i am a first time user of R Software.
> 
> I am trying to run a hierachical clustering of binding site similarities 
> of some ligands.. I need to use Single Linkage. I am trying to run a 
> command line version of the program. I already have a distance matrix of 
> similarity scores available as a text file. The output of clusters needs 
> to printed as a dendrogram. Can I choose the option to print the cluster 
> results as a *text file *, as well as to *view the tree as a PDF*? Has 
> anyone done something similar to this?
> 
> Any help will be great


The good news is that R can do everything you have asked. The bad news 
is that R takes time and patience to learn. Its not really like Perl or 
Java, and can be confusing for that reason alone.

You must read the 'S Poetry - Essentials Chapter' by P. Burns (R is very 
similar to S), and you should read the 'manual page' for all the 
functions you are likely to use (type "?some.function");

?read.table
?dist
?clust
?plot
?pdf


If you can read and absorb these you will be well on your way. However, 
  that will be very difficult for a beginner, so you should seek help on 
the R mailing list (see R web site for instructions) and perhaps in the 
R help channel irc://freenode.net/#R

Good luck!