Man pages for grafab/pergola
Toolbox for Polyploid Genetic Data
| addOffset | Add offset |
| allTrees | Creates all trees for distance |
| basesToGenotypes | Transform bases into genotypes |
| calcRec | Recombination frequencies computation |
| calcSarf | Calculates the SARF value of given input. |
| calcSarfDist | Calculates SARF |
| findChr | Find most equal chromosome in other map |
| getLeaves | Leaves from subtree |
| getNode | Get Node for leave |
| getSubtree | Subtrees from tree |
| makeAltOrd | Creates vectors with highly distant neighbors |
| makeTangle | Create a gray scale tanglegram |
| mapToDend | Transforming a map into a dendrogram |
| pairwRF | Pairwise recombination frequency calculation |
| pergola | Toolbox for polyploid genetic data |
| plotChr | Plotting one or two linkage maps |
| plotRf | Plot recombination frequencies |
| pullMap | Creates map object |
| sarfExt | Extends SARF criterion to neighborhood |
| shuffleInput | Randomize marker order and alleles within samples |
| simHexa | Hexaploid F2 population |
| simTetra | Tetraploid F2 population |
| sortLeafs | Chromosome wise leaf ordering |
| splitChr | Split markers into chromosomes |
| swapChrs | Swap chromosomes |
| switchChr | Switch Chromosomes |
| switchChrs | Switch Chromosomes |
| switchEntries | Switches entries in hclust object |
