APIS_2n {APIS}

APIS for diploids

Description

APIS for diploids

Usage

APIS_2n(
  offspring_genotype,
  sire_genotype,
  dam_genotype,
  method = "mendel",
  exclusion_threshold = NULL,
  error = 0.05,
  simulation_if_small = FALSE,
  number_offspring_simulated = max(0, 500 - nrow(offspring_genotype)),
  number_cores = 2,
  verbose = FALSE
)

Arguments

offspring_genotype

matrix of the offspring genotypes

sire_genotype

matrix of the sire genotypes

dam_genotype

matrix of the offspring genotypes

method

method : "mendel" i.e. likelihood or "exclusion" (default : "mendel"). Can also be "" to select the method a posteriori.

exclusion_threshold

threshold for "exclusion" method (default : NULL). Override the error parameter if not NULL

error

error accepted (default : 0.05)

simulation_if_small

simulate individuals (TRUE or FALSE)

number_offspring_simulated

number of offspring simulated (default : 500)

number_cores

number of cores

verbose

verbose

Value

list of 2 elements : a pedigree file and the log file

Examples

data("APIS_offspring")
data("APIS_sire")
data("APIS_dam")

assignment <- APIS_2n(offspring_genotype = APIS_offspring[1:35,1:50],
                      sire_genotype = APIS_sire[ ,1:50],
                      dam_genotype = APIS_dam[ ,1:50],
                      simulation_if_small = FALSE)