[R] Compare two distance matrices

From: Mattias de Hollander <mdehollander_at_gmail.com>
Date: Thu 06 Oct 2005 - 20:23:24 EST


Hi all,

I am trying to compare two distance matrices with R. I would like to create a XY plot of these matrices and do some linear regression on it. But, I am a bit new to R, so i have a few questions (I searched in the documentation with no success).
The first problem is loading a distance matrix into R. This matrix is the output of a the Phylip program Protdist and lookes like this:

    5

n_crassa    0.000000  0.690737  0.895257  0.882576  2.365386
c_neufor    0.690737  0.000000  0.956910  0.979988  2.103041
a_thaliana  0.895257  0.956910  0.000000  1.003668  2.724847
pompep      0.882576  0.979988  1.003668  0.000000  2.065202
s_cerevis 2.365386 2.103041 2.724847 2.065202 0.000000

    5

n_crassa    0.000000  0.739560  0.933986  0.861644  2.207467
c_neufor    0.739560  0.000000  0.988779  0.925168  1.941141
a_thaliana  0.933986  0.988779  0.000000  1.007803  2.415320
pompep      0.861644  0.925168  1.007803  0.000000  2.394490
s_cerevis 2.207467 1.941141 2.415320 2.394490 0.000000 .....

I tried with the scan() function to load the files, but with no success. How should i load in these files?

Second i saw there is package for distance matrices (http://stat.ethz.ch/R-manual/R-devel/library/stats/html/dist.html). I thought of using as.dist() to convert the files to a R dist matrix. I have not been able to try this, because the first step didn't succeed.

Is this the right approach, or is there any other way of comparing distance matrices with R?



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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Thu Oct 06 21:00:21 2005

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