Level 0 function that returns genotypes from the csd locus. See
SimParamBee
for more information about the csd locus and how
we have implemented it.
getCsdGeno(
x,
caste = NULL,
nInd = NULL,
dronesHaploid = TRUE,
collapse = FALSE,
simParamBee = NULL
)
getQueenCsdGeno(x, collapse = FALSE, simParamBee = NULL)
getFathersCsdGeno(
x,
nInd = NULL,
dronesHaploid = TRUE,
collapse = FALSE,
simParamBee = NULL
)
getVirginQueensCsdGeno(x, nInd = NULL, collapse = FALSE, simParamBee = NULL)
getWorkersCsdGeno(x, nInd = NULL, collapse = FALSE, simParamBee = NULL)
getDronesCsdGeno(
x,
nInd = NULL,
dronesHaploid = TRUE,
collapse = FALSE,
simParamBee = NULL
)
Pop-class
, Colony-class
, or
MultiColony-class
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"
numeric, for how many individuals; if NULL
all individuals
are taken; this can be useful as a test of sampling individuals
logical, return haploid result for drones?
logical, if the return value should be a single matrix with haplotypes of all the individuals
SimParamBee
, global simulation parameters
matrix with genotypes when x
is Pop-class
, list
of matrices with genotypes when x
is Colony-class
(list nodes named by caste) and list of a list of matrices with genotypes
when x
is MultiColony-class
, outer list is named by
colony id when x
is MultiColony-class
; NULL
when
x
is NULL
The returned genotypes are spanning multiple bi-allelic SNP of
a non-recombining csd locus / haplotype. In most cases you will want to use
getCsdAlleles
.
getQueenCsdGeno()
: Access csd genotypes of the queen
getFathersCsdGeno()
: Access csd genotypes of the fathers
getVirginQueensCsdGeno()
: Access csd genotypes of the virgin queens
getWorkersCsdGeno()
: Access csd genotypes of the virgin queens
getDronesCsdGeno()
: Access csd genotypes of the virgin queens
founderGenomes <- quickHaplo(nInd = 8, nChr = 1, segSites = 100)
SP <- SimParamBee$new(founderGenomes)
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 = 4)
#> 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
# Use getCsdGeno on a Population
getCsdGeno(getQueen(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdGeno(getWorkers(colony))
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Using dronesHaploid = TRUE returns drones as haploids instead of double haploids
getCsdGeno(getDrones(colony), nInd = 3, dronesHaploid = TRUE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Using dronesHaploid = FALSE returns drones as double haploids
getCsdGeno(getDrones(colony), nInd = 3, dronesHaploid = FALSE)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Use getCsdGeno on a Colony
getCsdGeno(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdGeno(colony, caste = "queen")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getQueenCsdGeno(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdGeno(colony, caste = "workers")
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getWorkersCsdGeno(colony)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
# Same aliases exist for all the castes!
# Use getCsdGeno on a MultiColony - same behaviour as for the Colony!
getCsdGeno(apiary)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found
getCsdGeno(apiary, nInd = 2)
#> Error in get(x = "SP", envir = .GlobalEnv): object 'SP' not found