Toolbox for Polyploid Genetic Data

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Documentation for package ‘pergola’ version 1.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.

Help Pages

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