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pergola (version 1.0)

Toolbox for Polyploid Genetic Data

Description

Provides tools for linkage mapping in polyploids. It implements the method PERGOLA, which is a fast, deterministic method to calculate the order of markers in a linkage group.

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Version

Install

install.packages('pergola')

Monthly Downloads

21

Version

1.0

License

GPL-3

Issues

1

Pull Requests

0

Stars

2

Forks

0

Maintainer

Fabian Grandke

Last Published

April 3rd, 2016

Functions in pergola (1.0)

bases2genotypes

Transform bases into genotypes
plotRf

Plot recombination frequencies
sarfExt

Extends SARF criterion to neighborhood
switchEntries

Switches entries in hclust 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.
switchChrs

Switch Chromosomes
simHexa

Hexaploid F2 population
calcSarfDist

Calculates SARF
getLeaves

Leaves from subtree
pullMap

Creates map object
getSubtree

Subtrees from tree
allTrees

Creates all trees for distance
makealtord

Creates vectors with highly distant neighbors
swapChrs

Swap chromosomes
map2dend

Transforming a map into a dendrogram
sortLeafs

Chromosome wise leaf ordering
calcSarf

Calculates the SARF value of given input.
simTetra

Tetraploid F2 population
pergola

Toolbox for polyploid genetic data
findChr

Find most equal chromosome in other map
pairwRF

Pairwise recombination frequency calculation
getNode

Get Node for leave
calcRec

Recombination frequencies computation
maketangle

Create a gray scale tanglegram
add_offset

Add offset
switchChr

Switch Chromosomes
plotChr

Plotting one or two linkage maps
splitChr

Split markers into chromosomes