pedigreeCross {AlphaSimR}

Pedigree cross

Description

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

The way in which the user supplied pedigree is used depends on the value of matchID. If matchID is TRUE, the IDs in the user supplied pedigree are matched against founderNames. If matchID is FALSE, founder individuals in the user supplied pedigree are randomly sampled from founderPop.

Usage

pedigreeCross(
  founderPop,
  id,
  mother,
  father,
  matchID = FALSE,
  maxCycle = 100,
  DH = NULL,
  nSelf = 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 if matchID=FALSE.

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.

matchID

indicates if the IDs in founderPop should be matched to the id argument. See details.

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.

nSelf

an optional vector indicating how many generations an individual should be selfed.

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

#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)