Access haplotypes for all segregating sites of individuals in a caste

Source: R/Functions_L0_auxilary.R

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

getSegSiteHaplo(
  x,
  caste = NULL,
  nInd = NULL,
  haplo = "all",
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

getQueenSegSiteHaplo(
  x,
  haplo = "all",
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getFathersSegSiteHaplo(
  x,
  nInd = NULL,
  haplo = "all",
  chr = NULL,
  dronesHaploid = TRUE,
  collapse = FALSE,
  simParamBee = NULL
)

getVirginQueensSegSiteHaplo(
  x,
  nInd = NULL,
  haplo = "all",
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getWorkersSegSiteHaplo(
  x,
  nInd = NULL,
  haplo = "all",
  chr = NULL,
  collapse = FALSE,
  simParamBee = NULL
)

getDronesSegSiteHaplo(
  x,
  nInd = NULL,
  haplo = "all",
  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

haplo

character, either "all" for all haplotypes or an integer for a single set of haplotypes, use a value of 1 for female haplotypes and a value of 2 for male haplotypes

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 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

  • getQueenSegSiteHaplo(): Access haplotype data for all segregating sites of the queen

  • getFathersSegSiteHaplo(): Access haplotype data for all segregating sites of fathers

  • getVirginQueensSegSiteHaplo(): Access haplotype data for all segregating sites of virgin queens

  • getWorkersSegSiteHaplo(): Access haplotype data for all segregating sites of workers

  • getDronesSegSiteHaplo(): Access haplotype data for all segregating sites of drones

See also

getSegSiteHaplo and pullSegSiteHaplo

Examples

founderGenomes <- quickHaplo(nInd = 4, nChr = 1, segSites = 50)
SP <- SimParamBee$new(founderGenomes)
SP$nThreads = 1L
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 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
getSegSiteHaplo(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
getSegSiteHaplo(queens)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found

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

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

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