sortLeafs: Chromosome wise leaf ordering

In grafab/pergola: Toolbox for Polyploid Genetic Data

Description

Calculates the optimal leaf ordering pairwise for all linkage groups.

Usage

sortLeafs(rf, df, method = "seriation", maxSarf = NULL)

Arguments

rf	Matrix of pairwise recombination frequencies.
df	Vector of cluster numbers, created by splitChr(). Zeros indicated filtered markers and will be ignored.
method	Name of method. Default: seriation (uses the optimal leaf ordering algorithm from the seriation package). Alternatives endlink (order.endlink from gclus) and endlink-global (ignores linkage groups).
maxSarf	Maximum number of neighbor to include into SARF extension.

Value

Vector of global marker order.

Examples

data(simTetra)
simTetrageno <- basesToGenotypes(simTetra, 4)
rfMat <- calcRec(simTetrageno, 4)
split <- splitChr(rfMat, nchr = 7)
sortLeafs(rfMat, split)

grafab/pergola documentation built on May 17, 2019, 8:18 a.m.