Toolbox for Polyploid Genetic Data


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Documentation for package ‘pergola’ version 1.0

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pergola-package Toolbox for polyploid genetic data
add_offset Add offset
bases2genotypes Transform bases into genotypes
calcRec Recombination frequencies computation
calcSarf Calculates the SARF value of given input.
maketangle Create a gray scale tanglegram
map2dend Transforming a map into a dendrogram
pergola Toolbox for polyploid genetic data
plotChr Plotting one or two linkage maps
plotRf Plot recombination frequencies
pullMap Creates map object
shuffleInput Randomize marker order and alleles within samples In simulated datasets, the order or markers and alleles within samples is often given. To remove any prior knowledge, that would not be available, the data should be randomized. Thus, the performance of our tool can be validated unbiased.
simHexa Hexaploid F2 population
simTetra Tetraploid F2 population
sortLeafs Chromosome wise leaf ordering
splitChr Split markers into chromosomes
swapChrs Swap chromosomes
switchChrs Switch Chromosomes