# [R] How to generate a distance matrix?

burgundy sauburn at yahoo.com
Fri Apr 30 10:12:52 CEST 2010

```Hi,

I'm trying to generate a distance matrix between sample pairs (example
below). I'm not very familiar with the loop command which I expect I will
need for this. The example below demosntrates what I'd like to get out of
the data - essentially, to calculate the proportion of positions where two
samples differ.
Any help much appreciated! Also, any notes on how the functions work would
be great!

Thanks!

Example input (note: comma indicates column separators, a:d are sample
names):

a,1,2,4,4
b,2,1,4,4
c,1,2,3,4
d,1,0,4,0

Identify positions which differ between pairwise comparisons of samples a:d
(score 1 for differ, 0 for shared in example below)
some comparisons are duplicates, e.g. ab and ba, and self-comparisons such
as aa or bb are obviously all "1", but these are neccessary to make the
matrix

aa,1,1,1,1
ab,1,1,0,0
ac,0,0,1,0
ba,1,1,0,0
bb,1,1,1,1
bc,1,1,1,0
etc... to dd

Calculate proportion of differing positions between pairwise comparisons
aa,0
ab,0.5
ac,0.25
ba,0.5
bb,0
bc,0.75
etc...to dd

prepare matrix (e.g. ab value plotted in [a,b]; ba value plotted in [b,a]
etc...)

a,b,c,d
a,0,0.5,0.25,0.5
b,0.5,0,0.75 etc...
c
d

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