APIS_3n: APIS for triploids

In APIS: Auto-Adaptive Parentage Inference Software Tolerant to Missing Parents

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
)

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

Value

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

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)

APIS documentation built on Nov. 23, 2023, 5:06 p.m.