Pedigree cross
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.
pedigreeCross( founderPop, id, mother, father, matchID = FALSE, founderNames = NULL, maxCycle = 100, DH = NULL, useFemale = TRUE, simParam = NULL )
founderPop |
|
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. |
founderNames |
names for individuals in the founder population. Must be provided when matchID=TRUE. |
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 |
#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)
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