Man pages for perfectphyloR
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')... |
