Calculates a, the number of an individual's alleles that are rare in each simulation.

Part of Genetic Value Analysis

Usage

calcA(alleles, threshold = 1L, byID = FALSE)

Arguments

alleles

a matrix with {id, parent, V1 ... Vn} providing the alleles an animal received during each simulation. The first 2 columns provide the animal ID and the parent the allele came from. Remaining columns provide alleles.

threshold

an integer indicating the maximum number of copies of an allele that can be present in the population for it to be considered rare. Default is 1.

byID

logical variable of length 1 that is passed through to eventually be used by alleleFreq(), which calculates the count of each allele in the provided vector. If byID is TRUE and ids are provided, the function will only count the unique alleles for an individual (homozygous alleles will be counted as 1).

Value

A matrix with named rows indicating the number of unique alleles an animal had during each round of simulation (indicated in columns).

Examples

library(nprcgenekeepr)
rare <- calcA(nprcgenekeepr::ped1Alleles, threshold = 3, byID = FALSE)