View source: R/data_conversion.R
allelic_list | R Documentation |
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
allelic_list(cs, ac, samp_type = "both")
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" |
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.
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
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