TEST2: Test for Symmetry of Matched DNA Sequences

In DNAseqtest: Generating and Testing DNA Sequences

Description

This function tests for symmetry between all the pairs of K matched DNA sequences.

Usage

TEST2(f)

Arguments

f	a 4^K array containing the observed divergence array N

Details

This function calculates Bowker's test for symmetry, Stuart's test for marginal symmetry and the test for internal symmetry. It depends on the 4^K observed divergence array N.

Value

A list of three lower triangle matrices

first	the lower triangle of the matrix contains (K-1) x (K-1) values shows Bowker's test between all the possible pairs of the K sequences
second	the lower triangle of the matrix contains (K-1) x (K-1) values shows Stuart's test between all the possible pairs of the K sequences
third	the lower triangle of the matrix contains (K-1) x (K-1) values shows the internal test between all the possible pairs of the K sequences

References

Lars Sommer Jermiin, Vivek Jayaswal, Faisal Ababneh, John Robinson (2008). Phylogenetic model evaluation. Bioinformatics, Volume 452 of the series Methods in Molecular Biology, 331-364.

Faisal Ababneh, Lars S Jermiin, Chunsheng Ma, John Robinson (2006). Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences. Bioinformatics, 22(10), 1225-1231.

See Also

Ntml, simapp, simemb, TEST3

Examples

merge2<-matrix(c(-1,-4,-3,2,-2,-5,1,3), 4, 2)
theta<-c(rep(.25,3), rep(.25,3), rep(.25,3), c(.2,.35,.79,.01,.93,.47),
3,.1,.5,.8)
F1<-gn(theta,merge2)
N1<-Ntml(1000,F1)
t2<-TEST2(N1)
t2

Example output

$Bowker.test
       1      2      3      4
2 0.3278                     
3 0.6403 0.8958              
4 0.0257 0.0039 0.9277       
5 0.4081 0.3335 0.8833 0.8104

$Stuart.test
       1      2      3      4
2 0.2326                     
3 0.7467 0.8420              
4 0.2985 0.5256 0.6677       
5 0.5102 0.3402 0.7241 0.5074

$Internal.test
       1      2      3      4
2 0.4499                     
3 0.3851 0.7023              
4 0.0134 0.0007 0.9507       
5 0.2811 0.3194 0.7907 0.8823

DNAseqtest documentation built on May 1, 2019, 9:51 p.m.