matchAfreq: Match Samples and Allele Frequencies

In innager/dcifer: Genetic Relatedness Between Polyclonal Infections

Match Samples and Allele Frequencies

Description

Checks if the list containing sample data is conformable to provided population allele frequencies and reformats it if needed.

Usage

matchAfreq(dsmp, afreq)

Arguments

dsmp	a list with each element corresponding to one sample.
afreq	a list of allele frequencies. Each element of the list corresponds to a locus.

Details

The function reorders loci and alleles in dsmp to match those in afreq and inserts alleles into dsmp if they are present in afreq and not in dsmp; doesn't handle cases when alleles are present in dsmp but not in afreq. Allele names are required for this procedure.

Value

A list of the same length as dsmp, with each element matching the lengths and the names of afreq and its elements.

See Also

readDat and readAfreq for reading in and reformating data.

Examples

afile  <- system.file("extdata", "MozAfreq.csv", package = "dcifer")
afreq2 <- readAfreq(afile, lvar = "locus", avar = "allele", fvar = "freq")
dsmp2  <- matchAfreq(dsmp, afreq2)

innager/dcifer documentation built on May 21, 2024, 1:23 a.m.