assignmentFortran {APIS}R Documentation

Assignment function to obtain the average Mendelian transmission probabilities using a Fortran library

Description

This function calculates the average Mendelian transmission probabilities

Usage

assignmentFortran(offspring, sire, dam, thresh = ncol(offspring),
  preselect.Parent = FALSE, nb.cores = 2, verbose = TRUE)

Arguments

offspring

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

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

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)

thresh

(default: ncol(offspring) 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

intermidiate pedigree

log file for Mendelian transmission probabilities

log file for exclusion

Examples

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

assignment <- assignmentFortran(APIS_offspring[1:50, ], APIS_sire, APIS_dam, verbose = FALSE)


[Package APIS version 1.0.1 Index]