Reconstruct Perfect Phylogenies from DNA Sequence Data


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Documentation for package ‘perfectphyloR’ version 0.2.1

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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.