computemap: Computes map distances

In behuang/mpMap: Multi-Parent RIL Genetic Analysis

Description

Given an mpcross object with a map order and matrix of recombination fractions, this function will estimate map positions, using the subdiagonal entries of the recombination fraction matrix and (optionally) other non-diagonal entries.

Usage

computemap(object, mapfx = c("haldane", "kosambi"), maxOffset = 1)

Arguments

object	Object of class mpcross
mapfx	Map function to convert recombination fractions to cM
maxOffset	Controls which regions of the recombination fraction matrix are used to estimate distances. Specify 1 for super-diagonal elements, 2 to use one additional set of diagonal entries, etc

Details

The distance between marker i and i+1 can be estimated as mapfunction(object$rf$theta[i, i+1]). Specifying maxOffset = 1 will use this method to estimate map distances. Specifying maxOffset = 2 will use mapfunction(object$rf$theta[i, i+2]), mapfunction(object$rf$theta[i, i+1]) and mapfunction(object$rf$theta[i+1, i+2]) to estimate the distances between markers i, i+1 and i+2 jointly. Similarly, larger values of maxOffset use recombination fractions between more distant markers in the estimation of map disatnce. All estimation is done using non-negative linear least squares

Value

An mpcross object is returned whose map component has been estimated based on the map order and matrix of recombination fractions. Missing recombination fractions are imputed either by filling in the closest non-missing value (missfx=1) or by averaging the distance between other nearby markers (missfx=2).

See Also

mpcross nnls

behuang/mpMap documentation built on May 12, 2019, 10:53 a.m.