Reconstruct Perfect Phylogenies from DNA Sequence Data

assoTest | Compute the user-provided association statistics |

buildDend | Build the tree for the window of SNVs. |

checkCompatible | Apply Four-Gamete Test to check the compatibility of a pair... |

createHapMat | Create an object of class 'hapMat' |

dCor | Compute distance correlation (dCor) coefficient two random... |

dCorTest | dCor test for similarity of two matrices |

dendToNewick | Convert a list data structure to Newick format |

distMatRcpp | This function computes the pair wise distances of tips... |

ex_hapMat_data | Example dataset |

ex_hapMatSmall_data | Example small dataset |

extractHaplos | Extract haplotypes and return it as a list from genotype... |

findSNVs | Find the window of SNVs at a focal point |

fourGamete | Four-Gamete Test |

getNextFromFocal | Next SNV from the focal point |

getNextLeftFocal | Expand the neighborhood to the left |

getNextRightFocal | Expand the neighborhood to the right |

getnSNVs | Number of SNVs |

HHGtest | HHG test for association of two distance matrices |

makeDend | Recursive partitioning of sequences at a focal point. |

makeNewickRec | Build the character string of nodes and haplotypes in Newick... |

makePartition | Recursively partition haplotype matrix |

mantelStat | This function performs Mantel test for correlation between... |

MantelTest | Mantel test for association of two distance matirces |

newNode | Create a list of child nodes |

noVariation | Check the variation in a SNV |

orderColsAncestry | Utility function needed by 'orderSNVs' |

orderSNVs | Order SNVs |

perfectphyloR-package | Reconstruct perfect phylogenies from DNA sequence data |

performTest | Perform the user-provided association test |

phenoDist | Phenotypic distances |

plotDend | Plot reconstructed dendrogram |

RandIndex | Rand Index |

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 |

RVcoeff | Compute RV coefficient to measure association of two distance... |

RVtest | RV test for association of two distance matrices |

selectWindow | Select a window of SNVs about the focal SNV. |

splitTips | Separate haplotype names for haplotypes that can not be... |

subsetHapMat | Subset hapMat |

tdend | True dendrogram object |

testAssoDist | Test the association between a comparator distance matrix,... |

testDendAssoRI | Tests Rand Index between a comparator dendrogram and... |

vcftohapMat | Create a 'hapMat' object from variant call format ('vcf')... |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.