Get csd alleles — getCsdAlleles • SIMplyBee

Level 0 function that returns alleles from the csd locus. See SimParamBee for more information about the csd locus.

getCsdAlleles(
  x,
  caste = NULL,
  nInd = NULL,
  allele = "all",
  dronesHaploid = TRUE,
  collapse = FALSE,
  unique = FALSE,
  simParamBee = NULL
)

getQueenCsdAlleles(
  x,
  allele = "all",
  unique = FALSE,
  collapse = FALSE,
  simParamBee = NULL
)

getFathersCsdAlleles(
  x,
  nInd = NULL,
  allele = "all",
  dronesHaploid = TRUE,
  unique = FALSE,
  collapse = FALSE,
  simParamBee = NULL
)

getVirginQueensCsdAlleles(
  x,
  nInd = NULL,
  allele = "all",
  unique = FALSE,
  collapse = FALSE,
  simParamBee = NULL
)

getWorkersCsdAlleles(
  x,
  nInd = NULL,
  allele = "all",
  unique = FALSE,
  collapse = FALSE,
  simParamBee = NULL
)

getDronesCsdAlleles(
  x,
  nInd = NULL,
  allele = "all",
  dronesHaploid = TRUE,
  unique = FALSE,
  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, for how many individuals; if NULL all individuals are taken; this can be useful as a test of sampling individuals
allele: character, either "all" for both alleles or an integer for a single allele, use a value of 1 for female allele and a value of 2 for male allele
dronesHaploid: logical, return haploid result for drones?
collapse: logical, if TRUE, the function will return a set of csd alleles across the entire population, colony, or multicolony (not separately for each caste when x is a colony or each caste of each colony when x is a multicolony. This is a way to get one single object as an output across castes or colonies. Note this has nothing to do with the colony collapse. It's like paste(..., collapse = TRUE). Default is FALSE. See examples about this behaviour.
unique: logical, return only the unique set of csd alleles. This argument interacts with collapse. Default is FALSE. See examples about this behaviour.
simParamBee: SimParamBee, global simulation parameters

Value

matrix with haplotypes when x is Pop-class, list of matrices with haplotypes when x is Colony-class

(list nodes named by caste) and list of a list of matrices with haplotypes when x is MultiColony-class, outer list is named by colony id when x is MultiColony-class; NULL when

x is NULL

Details

If both collapse and unique are TRUE, the function returns a unique set of csd alleles in the entire population, colony, or multicolony

Functions

getQueenCsdAlleles(): Access csd alleles of the queen
getFathersCsdAlleles(): Access csd alleles of the fathers
getVirginQueensCsdAlleles(): Access csd alleles of the virgin queens
getWorkersCsdAlleles(): Access csd alleles of the workers
getDronesCsdAlleles(): Access csd alleles of the drones

Examples

founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes, nCsdAlleles = 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

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

# Use getCsdAlleles on a Population
getCsdAlleles(getQueen(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(getWorkers(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Use getCsdAlleles on a Colony
getCsdAlleles(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(colony, caste = "queen")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getQueenCsdAlleles(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(colony, caste = "workers")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getWorkersCsdAlleles(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Same aliases exist for all the castes!

getCsdAlleles(colony, unique = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(colony, collapse = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(colony, collapse = TRUE, unique = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

# Use getCsdAlleles on a MultiColony
getCsdAlleles(apiary)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(apiary, unique = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(apiary, collapse = TRUE, unique = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdAlleles(apiary, nInd = 2)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found