AlphaSimR (version 0.10.0)

pedigreeCross: Pedigree cross

Description

Creates a Pop-class from a generic pedigree and a set of founder individuals.

Usage

pedigreeCross(founderPop, id, mother, father, maxCycle = 100,
  DH = NULL, useFemale = TRUE, simParam = NULL)

Arguments

founderPop

a Pop-class

id

a vector of unique identifiers for individuals in the pedigree. The values of these ids are seperate from the ids in the founderPop.

mother

a vector of identifiers for the mothers of individuals in the pedigree. Must match one of the elements in the id vector or they will be treated as unknown.

father

a vector of identifiers for the fathers of individuals in the pedigree. Must match one of the elements in the id vector or they will be treated as unknown.

maxCycle

the maximum number of loops to make over the pedigree to sort it.

DH

an optional vector indicating if an individual should be made a doubled haploid.

useFemale

If creating DH lines, should female recombination rates be used. This parameter has no effect if, recombRatio=1.

simParam

an object of 'SimParam' class

Examples

# NOT RUN {
#Create founder haplotypes
founderPop = quickHaplo(nInd=2, nChr=1, segSites=10)

#Set simulation parameters
SP = SimParam$new(founderPop)

#Create population
pop = newPop(founderPop, simParam=SP)

#Pedigree for a biparental cross with 7 generations of selfing
id = 1:10
mother = c(0,0,1,3:9)
father = c(0,0,2,3:9)
pop2 = pedigreeCross(pop, id, mother, father, simParam=SP)

# }