Man pages for maize-genetics/rPHG
R front-end for the practical haplotype graph
| brapiURL | Return URL path |
| brapiVersion | Return BrAPI version ID |
| buildHaplotypeGraph | Helper function to build HaplotypeGraph object |
| calcMutualInfo | Calculate mutual information for a given PHG data set |
| configFilePath | Return file path of configuration file |
| dbName | Return name of DB |
| dbType | Return type of DB |
| gvcfMetrics | Generate metrics for GVCF data |
| HaplotypeGraph-class | A HaplotypeGraph Class |
| HaplotypeGraph-validity | HaplotypeGraph validation |
| host | Return host data |
| httProtocol | Return protocol value |
| isDemo | Return demo state |
| javaMemoryAddress | Return 'rJava' reference object |
| javaRefObj | Return 'rJava' reference object |
| json2tibble | JSON to tibble converter |
| numberOfChromosomes | Return number of chromosomes |
| numberOfNodes | Return number of nodes |
| numberOfRefRanges | Return number of reference ranges |
| numberOfTaxa | Return number of taxa |
| numHaploPerRefRange | Return number of haplotypes per reference range |
| PHGCon-class | A PHGCon Class |
| phgConObj | Return a PHG connection object |
| PHGCon-validity | PHGCon validation |
| PHGDataSet-class | A PHGDataSet class |
| PHGLocalCon | Helper function to construct a 'PHGLocalCon' object |
| PHGLocalCon-class | A PHGLocalCon Class |
| PHGLocalCon-validity | PHGLocalCon validation |
| PHGMethod | Helper function to construct PHGMethod object |
| PHGMethod-class | A PHGMethod Class |
| phgMethodId | Return method ID |
| phgMethodType | Return method ID type |
| PHGMethod-validity | PHGMethod validation |
| PHGServerCon | PHGServerCon object constructor |
| PHGServerCon-class | An PHGServerCon Class |
| PHGServerCon-validity | BrAPI connection validation |
| phgType | Return type of PHG connection |
| plotDot | Generate dot plot from Anchor files |
| plotGraph | Plot a graph object |
| plotMutualInfo | Plot mutual information |
| port | Return port value |
| readHaplotypeIds | Return haplotype IDs |
| readPHGDataSet | Return a PHGDataSet |
| readRefRanges | Return reference ranges |
| readSamples | Return samples IDs |
| serverInfo | Return server information |
| show | Show method for PHGMethod objects |
| showPHGMethods | Return available PHG methods |
| startLogger | Start PHG logging information |
| taxaByNode | Return taxa info for haplotype IDs |
