pergola (version 1.0)

sortLeafs: Chromosome wise leaf ordering

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 <- bases2genotypes(simTetra, 4)
rfMat <- calcRec(simTetrageno, 4)
split <- splitChr(rfMat, nchr = 7)
sortLeafs(rfMat, split)