sortLeafs: Chromosome wise leaf ordering

Description Usage Arguments Value Examples

View source: R/sort.R

Description

Calculates the optimal leaf ordering pairwise for all linkage groups.

Usage

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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

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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.