nulls {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.