Dear All, It may sound a trivial question...but I couldn't find a simple solution in R: I'm working on all-against-all distance matrices, the values stored in these matrices representing measures of similarities between pair of proteins; these matrices can be considered representation of phylogenetic trees; I want to generate other matrices with the same randomly permuted distances....how can I shuffle these matrices ? thank you, Maria -- Maria Persico, PhD. student http://cbm.bio.uniroma2.it/~maria/ MINT database group Universita' di Tor Vergata, via della Ricerca scientifica 11 00133 Roma, Italy Tel +39 0672594315 (Supervisor's room) Fax +39 0672594766 Mobile phone: +393479715662 e-mail maria.persico at uniroma2.it

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" You can do something like this > m = matrix(1:144, 12, 12) > rowRandomIndex = sample(1:12) > colRandomIndex = sample(1:12) > m[rowRandomIndex, colRandomIndex] There must be more elegant ways to do this...but this should work. " Or try (replace=T i.e. bootstrap rather than permute is I think appropriate for your example >m = sample(m, length(m), replace=T) Stephen Henderson UCL, London WC1E 6BT Cheers, --TC On 3/19/07, prsmra01 at uniroma2.it <prsmra01 at="" uniroma2.it=""> wrote: > > Dear All, > > It may sound a trivial question...but I couldn't find a simple > solution in R: I'm working > on all-against-all distance matrices, the values stored in these > matrices representing > measures of similarities between pair of proteins; these matrices can > be considered > representation of phylogenetic trees; I want to generate other > matrices with the same > randomly permuted distances....how can I shuffle these matrices ? > > thank you, > > Maria > -- > Maria Persico, PhD. student > http://cbm.bio.uniroma2.it/~maria/ > MINT database group > Universita' di Tor Vergata, via della Ricerca scientifica 11 > 00133 Roma, Italy > Tel +39 0672594315 (Supervisor's room) > Fax +39 0672594766 > Mobile phone: +393479715662 > e-mail maria.persico at uniroma2.it > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}