titv: Number of pairwise transitions and transversions in an...
In spider: Species Identity and Evolution in R
Description
Usage
Arguments
Value
Author(s)
Examples
Description
Calculates the number of pairwise transitions and transversions between sequences.
Usage
1
titv(DNAbin)
Arguments
DNAbin
A DNA alignment of class ‘DNAbin’.
Value
A square matrix with dimensions of length(dat). The upper triangle contains the number of transversions. The lower triangle contains the number of transitions.
Author(s)
Samuel Brown <s_d_j_brown@hotmail.com>
Examples
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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")
spider documentation built on May 2, 2019, 5:16 p.m.
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Description Usage Arguments Value Author(s) Examples
Description
Calculates the number of pairwise transitions and transversions between sequences.
Usage
1 | titv(DNAbin)
|
Arguments
DNAbin |
A DNA alignment of class ‘DNAbin’. |
Value
A square matrix with dimensions of length(dat). The upper triangle contains the number of transversions. The lower triangle contains the number of transitions.
Author(s)
Samuel Brown <s_d_j_brown@hotmail.com>
Examples
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")
|
R Package Documentation
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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