joinMap2backcross: Genotype coding

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

Genotype coding

Description

Convert unphased genotypes encoded in the JoinMap format into the backcross configuration according to the CarthaGene or R/qtl formats. Genotypes are assumed to come from a bi-parental cross with outbred parents (population type "CP" in JoinMap) and the goal is to build two parental genetic maps via a pseudo-test-cross strategy (Grattapaglia and Sederoff, 1994). This function hence encodes genotypes as two backcrosses, one per parent. All locus will be duplicated and the suffix "_m" (for "mirror") added to their identifiers.

Usage

joinMap2backcross(
  x,
  alias.hom = "A",
  alias.het = "H",
  alias.dup = "Z",
  alias.miss = "-",
  parent.names = c("parent1", "parent2"),
  verbose = 1
)

Arguments

x	data frame in the JoinMap format, for instance from genoClasses2JoinMap; any column named "phase" or "clas" will be discarded from the start; a column named "seg" should be present (markers with missing segregation will be discarded); a column named "locus" should be present unless row names are given; all other columns are supposed to correspond to genotypes
alias.hom	alias to specify homozygotes ("A" for CarthaGene, 1 for R/qtl); should be different from alias.dup
alias.het	alias to specify heterozygotes ("H" for CarthaGene, 2 for R/qtl); should be different from alias.dup
alias.dup	alias used when duplicating the locus; should be different from both alias.hom and alias.het, but should be of the same mode (i.e. character or numeric)
alias.miss	alias to specify missing values
parent.names	vector containing the names of the parents
verbose	verbosity level (0/1/2)

Value

list of two matrices, one per parent

Author(s)

Timothee Flutre [aut], Agnes Doligez [ctb]

See Also

genoClasses2JoinMap, openCarthagene, setJoinMapPhasesFromParentalLinkGroups

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