APIS (version 2.0.7)

APIS_3n: APIS for triploids

Description

APIS for triploids

Usage

APIS_3n(
  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,
  t_recom = 0.5
)

Value

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

Arguments

offspring_genotype

matrix of the offspring genotypes

sire_genotype

matrix of the sire genotypes

dam_genotype

matrix of the dam 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) (default : TRUE)

number_offspring_simulated

number of offspring simulated (default : 500)

number_cores

number of cores

verbose

verbose

t_recom

recombination rate

Examples

data("APIS_offspring3n")
data("APIS_sire")
data("APIS_dam")
assignment <- APIS_3n(offspring_genotype = APIS_offspring3n[1:35,1:50],
                      sire_genotype = APIS_sire[ ,1:50],
                      dam_genotype = APIS_dam[ ,1:50],
                      simulation_if_small = FALSE)