API for ruidlpm/pathPhynder
A workflow for integrating ancient lineages into present-day Y-chromosome phylogenies.
| Global functions | |
|---|---|
| assignAncientCallsToBranch | Source code |
| calculate.prior | Source code |
| chooseBestPath | Source code |
| createPathScoresTab | Source code |
| determineHG | Source code |
| edge.loglik | Source code |
| estimatePlotDimensions | Source code Source code Source code |
| estimatePositionInBranch | Source code |
| force.ultrametric | Source code |
| getCountsforPath | Source code |
| getQueries | Source code |
| get_branches | Source code |
| get_nested_hg | Source code |
| get_relevant_line | Source code |
| get_score | Source code |
| get_vcf | Source code Source code Source code |
| getphylo_x | Source code |
| getphylo_y | Source code |
| impute | Source code Source code |
| makeBranchStatusTable | Source code |
| makeCountsEveryPath | Source code |
| makeHaplogroupStatusOutput | Source code |
| makeLongSNPtable | Source code |
| makePaths | Source code |
| makeReport | Source code |
| makeSNPStatusOutput | Source code |
| makeVCFsites | Source code |
| make_edge_df | Source code Source code |
| make_files | Source code |
| plotAncDerSNPTree | Source code Source code |
| plotBestPathTree | Source code |
| plot_final_tree | Source code Source code |
| plot_likes | Source code Source code |
| readBestNodes | Source code |
| read_in | Source code |
| traversePaths | Source code |
| tree.constructor | Source code Source code |
| trim_hg | Source code |
| writeBed | Source code |
| writeSampleTables | Source code |
