Hi Jeannine,
I'm just forwarding this Q&A back to the r-help list, you'll get more
eyes on it and other people might have better solutions.
Answers inline:
On Sep 11, 2009, at 12:25 PM, Jeannine Cavender-Bares wrote:
Dear Steve,
Greetings! You helped me earlier this summer with an R question in
response to a message Brian McCarthy put out on the listserv. I was
wondering if you happen to know the answer to the following question
or if you can explain how I subscribe to the listserv. Can one just
send a message to r-h...@r-project.org?
You can subscribe to the listserv from here:
https://stat.ethz.ch/mailman/listinfo/r-help
Here goes:
How does one convert a triangular distance matrix into a single
column distance matrix?: e.g.,
traingular:
A B C
A na na na
B 1 na na
C 0 1 na
single column:
BA 1
CA 0
CB 1
Getting the distances from your matrix is pretty straightforward since
they're all in the lower triangle of the matrix, see: ?lower.tri
R> m <- matrix(c(NA,1,0,NA,NA,1,NA,NA,NA), 3)
R> dimnames(m) <- list(c('A','B','C'), c('A','B','C'))
R> m[lower.tri(m)]
[1] 1 0 1
Getting the names for the distances is a bit more tricky. I'm trying
to do that with the "expand.grid" function, check it out to see how it
works: ?expand.grid
R> who.vs.who <- expand.grid(rownames(m), rownames(m))
R> who.vs.who
Var1 Var2
1 A A
2 B A
3 C A
4 A B
5 B B
6 C B
7 A C
8 B C
9 C C
We can use the same index generated by ``lower.tri(m)`` to get the
names of the rows vs cols since R stores the elements of a matrix in
column major order[1] (note that when I created the matrix ``m``, I
used a vector that filled a matrix column by column). When you use a
single integer to index into a matrix, it calculates which position to
pull out in the same (column major) order, so:
* ``m[1]`` is really element m[1,1]
* ``m[2]`` is really element m[2,1], etc ...
So now:
R> who.vs.who[lower.tri(m),]
Var1 Var2
2 B A
3 C A
6 C B
... almost there, no just put it together:
R> dist <- m[lower.tri(m)]
R> who <- who.vs.who[lower.tri(m),]
R> names(dist) <- paste(who[,1], who[,2], sep=".vs.")
R> dist
B.vs.A C.vs.A C.vs.B
1 0 1
HTH,
-steve
[1] Column major format:
http://en.wikipedia.org/wiki/Row-major_order#Column-major_order
--
Steve Lianoglou
Graduate Student: Computational Systems Biology
| Memorial Sloan-Kettering Cancer Center
| Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact
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