Wouldn't the ?dist
function help you ? ----------------Contact Details:------------------------------------------------------- Contact me: tal.gal...@gmail.com | 972-52-7275845 Read me: www.talgalili.com (Hebrew) | www.biostatistics.co.il (Hebrew) | www.r-statistics.com (English) ---------------------------------------------------------------------------------------------- On Fri, Apr 30, 2010 at 11:12 AM, burgundy <saub...@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. > [[alternative HTML version deleted]] ______________________________________________ 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.
