allelic_list: Create genotype lists for each locus
Description
Uses the allele counts from a_freq_list and the cleaned short-format output of
tcf2long to generate a nested list of individual genotypes for each locus
Usage
allelic_list(cs, ac, samp_type = "both")
Value
allelic_list returns a two-component nested list, with data stored as character
names of alleles ($chr) or as integer indices for the alleles ($int). Both forms contain lists
representing to loci, with two component vectors corresponding to gene copies a and b.
Arguments
cs
a clean short genetic data matrix; the second element of the
output from tcf2long. Must have a column of individual identifiers, named "indiv"
ac
allele counts from a_freq_list
samp_type
choose which sample types of individuals to include in output:
"mixture", "both", or "reference"
example(a_freq_list)
ale_cs <- ale_long$clean_short
# Get the vectors of gene copies a and b for all loci in integer index formale_alle_list <- allelic_list(ale_cs, ale_ac)$int