calcA: Calculates a, the number of an individual's alleles that are rare in
each simulation.
Description
Part of Genetic Value Analysis
Usage
calcA(alleles, threshold = 1, 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).