nulls: Estimation of allele frequencies under genotyping failure.

In genepop: Population Genetic Data Analysis Using Genepop

Estimation of allele frequencies under genotyping failure.

Description

Estimates allele frequencies (and failure rate if relevant) under dfferent assumptions: maximum likelihood assuming that there is null allele (default method), maximum likelihood assuming that apparent nulls are technical failures independent of genotype ('ApparentNulls'), and Brookfield's (1996) estimator ('B96'). See this section of the Genepop executable documentation for more information on the statistical methods. Genepop takes the allele with the highest number for a given locus across all populations as the null allele. For example, if you have 4 alleles plus a null allele, a null homozygote individual should be indicated as e.g. 0505 or 9999 in the input file.

Usage

nulls(
  inputFile,
  outputFile = "",
  settingsFile = "",
  nullAlleleMethod = "",
  CIcoverage = 0.95,
  verbose = interactive()
)

Arguments

inputFile	The path of the input file, in Genepop format
outputFile	character: The path of the output file
settingsFile	character: The path of the settings file
nullAlleleMethod	character: 'ApparentNulls', 'B96' or anything else (default method).
CIcoverage	numeric: The coverage probability of confidence interval
verbose	logical: whether to print some information

Value

The path of the output file is returned invisibly.

genepop documentation built on Jan. 22, 2023, 1:07 a.m.