Access QTL haplotypes of individuals in a caste

Source: R/Functions_L0_auxilary.R

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

getQtlHaplo(
  x,
  caste = NULL,
  nInd = NULL,
  trait = 1,
  haplo = "all",
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

getQueenQtlHaplo(
  x,
  trait = 1,
  haplo = "all",
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getFathersQtlHaplo(
  x,
  nInd = NULL,
  trait = 1,
  haplo = "all",
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

getVirginQueensQtlHaplo(
  x,
  nInd = NULL,
  trait = 1,
  haplo = "all",
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getWorkersQtlHaplo(
  x,
  nInd = NULL,
  trait = 1,
  haplo = "all",
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getDronesQtlHaplo(
  x,
  nInd = NULL,
  trait = 1,
  haplo = "all",
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

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 haplotypes to retrieve

haplo

character, either "all" for all haplotypes or an integer for a single set of haplotypes, use a value of 1 for female haplotypes and a value of 2 for male haplotypes

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 haplotypes of all the individuals

simParamBee

SimParamBee, global simulation parameters

Value

matrix with haplotypes when x is Colony-class

and list of matrices with haplotypes when x is

MultiColony-class, named by colony id when x is

MultiColony-class

Functions

  • getQueenQtlHaplo(): Access QTL haplotype data of the queen

  • getFathersQtlHaplo(): Access QTL haplotype data of fathers

  • getVirginQueensQtlHaplo(): Access QTL haplotype data of virgin queens

  • getWorkersQtlHaplo(): Access QTL haplotype of workers

  • getDronesQtlHaplo(): Access QTL haplotype data of drones

See also

getQtlHaplo and pullQtlHaplo as well as vignette(topic = "QuantitativeGenetics", package = "SIMplyBee")

Examples

founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 50)
SP <- SimParamBee$new(founderGenomes)
SP$addTraitA(nQtlPerChr = 10)
basePop <- createVirginQueens(founderGenomes)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

drones <- createDrones(x = basePop[1], nInd = 200)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
droneGroups <- pullDroneGroupsFromDCA(drones, n = 10, nDrones = nFathersPoisson)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Create a Colony and a MultiColony class
colony <- createColony(x = basePop[2])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- cross(colony, drones = droneGroups[[1]])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- buildUp(x = colony, nWorkers = 6, nDrones = 3)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
colony <- addVirginQueens(x = colony, nInd = 5)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

apiary <- createMultiColony(basePop[3:4], n = 2)
#> Error in createMultiColony(basePop[3:4], n = 2): object 'basePop' not found
apiary <- cross(apiary, drones = droneGroups[c(2, 3)])
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
apiary <- buildUp(x = apiary, nWorkers = 6, nDrones = 3)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
apiary <- addVirginQueens(x = apiary, nInd = 5)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Input is a population
getQtlHaplo(x = getQueen(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
queens <- getQueen(apiary, collapse = TRUE)
#> Error in is(x, class2 = "Colony"): object 'apiary' not found
getQtlHaplo(queens)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Input is a Colony
getQtlHaplo(colony, caste = "queen")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getQueenQtlHaplo(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

getQtlHaplo(colony, caste = "workers", nInd = 3)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getWorkersQtlHaplo(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Same aliases exist for all the castes!

# Get haplotypes for all individuals
getQtlHaplo(colony, caste = "all")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Get all haplotypes in a single matrix
getQtlHaplo(colony, caste = "all", collapse = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Input is a MultiColony - same behaviour as for the Colony
getQtlHaplo(apiary, caste = "queen")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getQueenQtlHaplo(apiary)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Get the haplotypes of all individuals either by colony or in a single matrix
getQtlHaplo(apiary, caste = "all")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getQtlHaplo(apiary, caste = "all", collapse = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found