APIS {APIS}R Documentation

APIS function that assigns with observed data

Description

This function performs the APIS procedure

Usage

APIS(off.genotype, sire.genotype, dam.genotype, error = 0,
  exclusion.threshold = ncol(off.genotype), preselect.Parent = FALSE,
  nb.cores = 2, verbose = TRUE)

Arguments

off.genotype

Offspring genotypes | Matrix (n*p) where n = number of individuals p = number of markers rownames(offspring) = labels of offspring marker coding = "All1/All2" example: "A/A", "A/B", "NA/NA" (for missing genotype)

sire.genotype

Sire genotypes | Matrix (n*p) where n = number of individuals p = number of markers rownames(sire) = labels of sires marker coding = "All1/All2" example: "A/A", "A/B", "NA/NA" (for missing genotype)

dam.genotype

Dam genotypes | Matrix (n*p) where n = number of individuals p = number of markers rownames(dam) = labels of dams marker coding = "All1/All2" example: "A/A", "A/B", "NA/NA" (for missing genotype)

error

(default: 0) The assignment error rate accepted by the user

exclusion.threshold

(default: ncol(off.genotype)) Threshold for exclusion (number of mismatches allowed)

preselect.Parent

(default: FALSE) Preselection of parents. Can be FALSE, an integer or a vector of two integers (number of sires, numbers of dams)

nb.cores

(default: 2) Number of cores to use. If you have more than 2 cores, you can use the "parallel" function detectCores()

verbose

(default : TRUE) Display the process of the function on the console.

Value

pedigree

a log file

Examples

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

result <- APIS(off.genotype = APIS_offspring[1:50, ],
               sire.genotype = APIS_sire,
               dam.genotype = APIS_dam,
               error = 0.05,
               verbose = FALSE)


[Package APIS version 1.0.1 Index]