Man pages for perfectphyloR
Reconstruct Perfect Phylogenies from DNA Sequence Data

assoTestCompute the user-provided association statistics
buildDendBuild the tree for the window of SNVs.
checkCompatibleApply Four-Gamete Test to check the compatibility of a pair...
createHapMatCreate an object of class 'hapMat'
dCorCompute distance correlation (dCor) coefficient two random...
dCorTestdCor test for similarity of two matrices
dendToNewickConvert a list data structure to Newick format
distMatRcppThis function computes the pair wise distances of tips...
ex_hapMat_dataExample dataset
ex_hapMatSmall_dataExample small dataset
extractHaplosExtract haplotypes and return it as a list from genotype...
findSNVsFind the window of SNVs at a focal point
fourGameteFour-Gamete Test
getNextFromFocalNext SNV from the focal point
getNextLeftFocalExpand the neighborhood to the left
getNextRightFocalExpand the neighborhood to the right
getnSNVsNumber of SNVs
HHGtestHHG test for association of two distance matrices
makeDendRecursive partitioning of sequences at a focal point.
makeNewickRecBuild the character string of nodes and haplotypes in Newick...
makePartitionRecursively partition haplotype matrix
mantelStatThis function performs Mantel test for correlation between...
MantelTestMantel test for association of two distance matirces
newNodeCreate a list of child nodes
noVariationCheck the variation in a SNV
orderColsAncestryUtility function needed by 'orderSNVs'
orderSNVsOrder SNVs
perfectphyloR-packageReconstruct perfect phylogenies from DNA sequence data
performTestPerform the user-provided association test
phenoDistPhenotypic distances
plotDendPlot reconstructed dendrogram
RandIndexRand Index
RandIndexTestRand Index Test
rdistMatrixRank-based distances between haplotypes in a given partition
reconstructPPReconstruct the perfect phylogeny at a given focal SNV
reconstructPPregionReconstruct perfect phylogeny sequencce across a region
RVcoeffCompute RV coefficient to measure association of two distance...
RVtestRV test for association of two distance matrices
selectWindowSelect a window of SNVs about the focal SNV.
splitTipsSeparate haplotype names for haplotypes that can not be...
subsetHapMatSubset hapMat
tdendTrue dendrogram object
testAssoDistTest the association between a comparator distance matrix,...
testDendAssoRITests Rand Index between a comparator dendrogram and...
vcftohapMatCreate a 'hapMat' object from variant call format ('vcf')...
perfectphyloR documentation built on March 8, 2021, 9:06 a.m.