calcSarf: Calculates the SARF value of given input.

In grafab/pergola: Toolbox for Polyploid Genetic Data

Description

The sum of adjecent recombination frequency (SARF) is a measure of how well the marker order is. This function calculates it for a given matrix of pairwise recombination frequencies and marker order. The SARF criterion can be extended to a neighborhood > 1.

Usage

calcSarf(rf, ord = 1:(ncol(rf)), n = 1)

Arguments

rf	Matrix of pairwise recombination frequencies.
ord	Vector with marker order.
n	Number of neighbors, which are included in the calculation.

Value

Single numeric value, which is the result of the SARF calculation.

References

Liu, B.H. 1998, Statistical genomics: linkage, mapping, and QTL analysis.

Examples

data(simTetra)
simTetrageno <- basesToGenotypes(simTetra, 4)
rfMat <- calcRec(simTetrageno, 4)
split <- splitChr(rfMat, nchr = 7)
split <- sortLeafs(rfMat, split)
calcSarf(rfMat, split$order, n = 1)
calcSarf(rfMat, split$order, n = 2)
calcSarf(rfMat, split$order, n = 3)

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