Access SNP array genotypes of individuals in a caste

Source: R/Functions_L0_auxilary.R

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

getSnpGeno(
  x,
  caste = NULL,
  nInd = NULL,
  snpChip = 1,
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

getQueenSnpGeno(
  x,
  snpChip = 1,
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getFathersSnpGeno(
  x,
  nInd = NULL,
  snpChip = 1,
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

getVirginQueensSnpGeno(
  x,
  nInd = NULL,
  snpChip = 1,
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getWorkersSnpGeno(
  x,
  nInd = NULL,
  snpChip = 1,
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getDronesSnpGeno(
  x,
  nInd = NULL,
  snpChip = 1,
  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

snpChip

numeric, indicates which SNP array 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

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

  • getQueenSnpGeno(): Access SNP array genotype data of the queen

  • getFathersSnpGeno(): Access SNP array genotype data of fathers

  • getVirginQueensSnpGeno(): Access SNP array genotype data of virgin queens

  • getWorkersSnpGeno(): Access SNP array genotype data of workers

  • getDronesSnpGeno(): Access SNP array genotype data of drones

See also

getSnpGeno and pullSnpGeno

Examples

founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 50)
SP <- SimParamBee$new(founderGenomes)
SP$addSnpChip(nSnpPerChr = 5)
basePop <- createVirginQueens(founderGenomes)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

drones <- createDrones(x = basePop[1], nInd = 1000)
#> 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
getSnpGeno(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
getSnpGeno(queens)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

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

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

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