getQtlGeno: Access QTL genotypes of individuals in a caste

Description

Level 0 function that returns QTL genotypes of individuals in a caste.

Usage

getQtlGeno(
  x,
  caste = NULL,
  nInd = NULL,
  trait = 1,
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)
getQueenQtlGeno(x, trait = 1, chr = NULL, collapse = FALSE, simParamBee = NULL)
getFathersQtlGeno(
  x,
  nInd = NULL,
  trait = 1,
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)
getVirginQueensQtlGeno(
  x,
  nInd = NULL,
  trait = 1,
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)
getWorkersQtlGeno(
  x,
  nInd = NULL,
  trait = 1,
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)
getDronesQtlGeno(
  x,
  nInd = NULL,
  trait = 1,
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

Value

matrix with genotypes when x is Colony-class and list of matrices with genotypes when x is

MultiColony-class, named by colony id when x is

MultiColony-class

Arguments

x: Pop-class, Colony-class, or MultiColony-class
caste: NULL or character, NULL when x is a Pop-class, and character when x is a Colony-class or MultiColony-class with the possible values of "queen", "fathers", "workers", "drones", "virginQueens", or "all"
nInd: numeric, number of individuals to access, if NULL all individuals are accessed, otherwise a random sample
trait: numeric (trait position) or character (trait name), indicates which trait's QTL genotypes to retrieve
chr: numeric, chromosomes to retrieve, if NULL, all chromosome are retrieved
dronesHaploid: logical, return haploid result for drones?
collapse: logical, if the return value should be a single matrix with genotypes of all the individuals
simParamBee: SimParamBee, global simulation parameters

Functions

getQueenQtlGeno(): Access QTL genotype data of the queen
getFathersQtlGeno(): Access QTL genotype data of fathers
getVirginQueensQtlGeno(): Access QTL genotype data of virgin queens
getWorkersQtlGeno(): Access QTL genotype data of workers
getDronesQtlGeno(): Access QTL genotype data of drones

Examples

Run this code

founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 50)
SP <- SimParamBee$new(founderGenomes)
SP$nThreads = 1L
SP$addTraitA(nQtlPerChr = 10)
basePop <- createVirginQueens(founderGenomes)

drones <- createDrones(x = basePop[1], nInd = 200)
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)

# Create a Colony and a MultiColony class
colony <- createColony(x = basePop[2])
colony <- cross(colony, drones = droneGroups[[1]])
colony <- buildUp(x = colony, nWorkers = 6, nDrones = 3)
colony <- addVirginQueens(x = colony, nInd = 5)

apiary <- createMultiColony(basePop[3:4], n = 2)
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
apiary <- buildUp(x = apiary, nWorkers = 6, nDrones = 3)
apiary <- addVirginQueens(x = apiary, nInd = 5)

# Input is a population
getQtlGeno(x = getQueen(colony))
queens <- getQueen(apiary, collapse = TRUE)
getQtlGeno(queens)

# Input is a colony
getQtlGeno(colony, caste = "queen")
getQueenQtlGeno(colony)

getQtlGeno(colony, caste = "workers", nInd = 3)
getWorkersQtlGeno(colony)
# Same aliases exist for all the castes!

# Get genotypes for all individuals
getQtlGeno(colony, caste = "all")
# Get all haplotypes in a single matrix
getQtlGeno(colony, caste = "all", collapse = TRUE)

# Input is a MultiColony - same behaviour as for the Colony!
getQtlGeno(apiary, caste = "queen")
getQueenQtlGeno(apiary)

# Get the genotypes of all individuals either by colony or in a single matrix
getQtlGeno(apiary, caste = "all")
getQtlGeno(apiary, caste = "all", collapse = TRUE)