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.