allelic_list {rubias} | R Documentation |
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")
Arguments
cs |
a clean short genetic data matrix; the second element of the
output from |
ac |
allele counts from a_freq_list |
samp_type |
choose which sample types of individuals to include in output: "mixture", "both", or "reference" |
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.
Examples
example(a_freq_list)
ale_cs <- ale_long$clean_short
# Get the vectors of gene copies a and b for all loci in integer index form
ale_alle_list <- allelic_list(ale_cs, ale_ac)$int
[Package rubias version 0.3.4 Index]