From: Mattias de Hollander <mdehollander_at_gmail.com>

Date: Thu 06 Oct 2005 - 20:23:24 EST

R-help@stat.math.ethz.ch mailing list

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

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 2.065202s_cerevis 2.365386 2.103041 2.724847 2.065202 0.000000

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 2.394490s_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?

R-help@stat.math.ethz.ch mailing list

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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