R help - Apr 2010 - How to generate a distance matrix?

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
ad,0,1,0,1
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
ad,0.5
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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Wouldn't the

?dist

function help you ?



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On Fri, Apr 30, 2010 at 11:12 AM, burgundy <sauburn@yahoo.com> wrote:
>
> 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
> ad,0,1,0,1
> 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
> ad,0.5
> 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
>
>
>
>
> --
> View this message in context:
>
http://r.789695.n4.nabble.com/How-to-generate-a-distance-matrix-tp2076600p2076600.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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