setJoinMapPhasesFromParentalLinkGroups: Genotype coding

In timflutre/rutilstimflutre: Timothee Flutre's personal R code

Genotype coding

Description

Set linkage phases in the JoinMap format from two sets of parental linkage groups. This function is tested only for segregation types <hkxhk>, <lmxll> and <nnxnp>, that is, in the case of bi-allelic SNPs segregating in a cross of outbred parents.

Usage

setJoinMapPhasesFromParentalLinkGroups(x, lg.par1, lg.par2)

Arguments

x	data frame in the JoinMap format, for instance from genoClasses2JoinMap; row names should contain locus names; the first column should be "seg"; any column(s) "phase" or "clas" already existing will be discarded; other columns should contain genotype data
lg.par1	linkage groups of the first parent (usually the mother) as a data frame with one row per marker and at least two columns named "linkage.group" and "locus"; "mirror" markers should have suffix "_m" as done by joinMap2backcross
lg.par2	linkage groups of the second parent (usually the father) as a data frame with one row per marker and at least two columns named "linkage.group" and "locus"; "mirror" markers should have suffix "_m" as done by joinMap2backcross

Value

data frame in the JoinMap format with a "phase" column

Author(s)

Timothee Flutre

timflutre/rutilstimflutre documentation built on Feb. 7, 2024, 8:17 a.m.