getIbdHaplo: Access IBD haplotypes of individuals in a caste

Description

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

Usage

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
)

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

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

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

Examples

Run this code

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)

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
getIbdHaplo(x = getQueen(colony))
queens <- getQueen(apiary, collapse = TRUE)
getIbdHaplo(queens)

# Input is a colony
getIbdHaplo(x = colony, caste = "queen")
getQueenIbdHaplo(colony)

getIbdHaplo(colony, caste = "workers", nInd = 3)
getWorkersIbdHaplo(colony)
# Same aliases exist for all castes!

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

# Input is a MultiColony
getIbdHaplo(x = apiary, caste = "queen")
getQueenIbdHaplo(apiary)
# Or collapse all the haplotypes into a single matrix
getQueenIbdHaplo(apiary, collapse = TRUE)

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