Match Samples and Allele Frequencies

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

Usage

matchAfreq(dsmp, afreq, minfreq = 1e-04)

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.

minfreq

an allele frequency to assign to alleles that are present in dsmp but not in afreq.

Value

A named list of length 2 containing updated and matching dsmp and afreq.

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.

See also

readDat and readAfreq for reading in and reformating data.

Examples

afile  <- system.file("extdata", "MozAfreq.csv", package = "dcifer")
afreq  <- readAfreq(afile, lvar = "locus", avar = "allele", fvar = "freq")
da_upd <- matchAfreq(dsmp, afreq, minfreq = 1e-3)
dsmp2  <- da_upd$dsmp
afreq2 <- da_upd$afreq