Access IBD haplotypes of individuals in a caste

Source: R/Functions_L0_auxilary.R

Level 0 function that returns IBD (identity by descent) haplotypes of individuals in a caste.

getIbdHaplo(
  x,
  caste = NULL,
  nInd = NULL,
  chr = NULL,
  snpChip = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

getQueenIbdHaplo(
  x,
  chr = NULL,
  snpChip = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getFathersIbdHaplo(
  x,
  nInd = NULL,
  chr = NULL,
  snpChip = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

getVirginQueensIbdHaplo(
  x,
  nInd = NULL,
  chr = NULL,
  snpChip = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getWorkersIbdHaplo(
  x,
  nInd = NULL,
  chr = NULL,
  snpChip = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getDronesIbdHaplo(
  x,
  nInd = NULL,
  chr = NULL,
  snpChip = 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

chr

numeric, chromosomes to retrieve, if NULL, all chromosome are retrieved

snpChip

integer, indicating which SNP array loci are to be retrieved, if NULL, all sites 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

  • getQueenIbdHaplo(): Access IBD haplotype data of the queen

  • getFathersIbdHaplo(): Access IBD haplotype data of fathers

  • getVirginQueensIbdHaplo(): Access IBD haplotype data of virgin queens

  • getWorkersIbdHaplo(): Access IBD haplotype data of workers

  • getDronesIbdHaplo(): Access IBD haplotype data of drones

See also

getIbdHaplo and pullIbdHaplo

Examples

founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 50)
SP <- SimParamBee$new(founderGenomes)
SP$nThreads = 1L
SP$setTrackRec(TRUE)
SP$setTrackPed(isTrackPed = TRUE)
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 get(x = "SP", envir = .GlobalEnv): object 'SP' 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
getIbdHaplo(x = getQueen(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
queens <- getQueen(apiary, collapse = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getIbdHaplo(queens)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

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

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

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

# Input is a MultiColony
getIbdHaplo(x = apiary, caste = "queen")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getQueenIbdHaplo(apiary)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Or collapse all the haplotypes into a single matrix
getQueenIbdHaplo(apiary, collapse = TRUE)
#> 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
getIbdHaplo(apiary, caste = "all")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getIbdHaplo(apiary, caste = "all", collapse = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found