perfectphyloR-package |
Reconstruct perfect phylogenies from DNA sequence data |
createHapMat |
Create an object of class 'hapMat' |
dCorTest |
dCor test for similarity of two matrices |
ex_hapMatSmall_data |
Example small dataset |
ex_hapMat_data |
Example dataset |
HHGtest |
HHG test for association of two distance matrices |
MantelTest |
Mantel test for association of two distance matirces |
perfectphyloR |
Reconstruct perfect phylogenies from DNA sequence data |
phenoDist |
Phenotypic distances |
plotDend |
Plot reconstructed dendrogram |
RandIndexTest |
Rand Index Test |
rdistMatrix |
Rank-based distances between haplotypes in a given partition |
reconstructPP |
Reconstruct the perfect phylogeny at a given focal SNV |
reconstructPPregion |
Reconstruct perfect phylogeny sequencce across a region |
RVtest |
RV test for association of two distance matrices |
tdend |
True dendrogram object |
testAssoDist |
Test the association between a comparator distance matrix, and the reconstructed dendrograms across a genomic region |
testDendAssoRI |
Tests Rand Index between a comparator dendrogram and reconstructed dendrograms |
vcftohapMat |
Create a 'hapMat' object from variant call format ('vcf') file. |