getSegSiteGeno {SIMplyBee}

Access genotypes for all segregating sites of individuals in a caste

Description

Level 0 function that returns genotypes for all segregating sites of individuals in a caste.

Usage

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

getQueenSegSiteGeno(x, chr = NULL, collapse = FALSE, simParamBee = NULL)

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

getVirginQueensSegSiteGeno(
  x,
  nInd = NULL,
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getWorkersSegSiteGeno(
  x,
  nInd = NULL,
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getDronesSegSiteGeno(
  x,
  nInd = NULL,
  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

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

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

Functions

• getQueenSegSiteGeno(): Access genotype data for all segregating sites of the queen

• getFathersSegSiteGeno(): Access genotype data for all segregating sites of fathers

• getVirginQueensSegSiteGeno(): Access genotype data for all segregating sites of virgin queens

• getWorkersSegSiteGeno(): Access genotype data for all segregating sites of workers

• getDronesSegSiteGeno(): Access genotype data for all segregating sites of drones

See Also

getSegSiteGeno and pullSegSiteGeno

Examples

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

drones <- createDrones(x = basePop[1], nInd = 1000)
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
getSegSiteGeno(x = getQueen(colony))
queens <- getQueen(apiary, collapse = TRUE)
getSegSiteGeno(queens)

# Input is a colony
getSegSiteGeno(colony, caste = "queen")
getQueenSegSiteGeno(colony)

getSegSiteGeno(colony, caste = "workers", nInd = 3)
getWorkersSegSiteGeno(colony)
# same aliases exist for all the castes!

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

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

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