Description Usage Arguments Value Author(s) Examples
Calculates the number of pairwise transitions and transversions between sequences.
1 | titv(DNAbin)
|
DNAbin |
A DNA alignment of class ‘DNAbin’. |
A square matrix with dimensions of length(dat)
. The upper triangle contains the number of transversions. The lower triangle contains the number of transitions.
Samuel Brown <s_d_j_brown@hotmail.com>
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 | data(dolomedes)
subs <- titv(dolomedes)
#Transversions
subs[upper.tri(subs)]
tv <- t(subs)
tv <- tv[lower.tri(tv)]
#Transitions
ti <- subs[lower.tri(subs)]
#Saturation plot
doloDist <- dist.dna(dolomedes)
plot(doloDist, ti, type="p", pch=19, col="blue",
main="Saturation plot of number of transitions and transversions\n
against K2P distance. Red: transversions. Blue: transitions")
points(doloDist, tv, pch=19, col="red")
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