View source: R/genetic_diversity.R
proportion_of_polymorphic_loci | R Documentation |
Estimate genome-wide proportion of polymorphic loci in a population
proportion_of_polymorphic_loci(
cnr,
exclude.chr = c("X", "Y"),
monomorphic.threshold = 0.95,
noise.threshold = 0.1,
chrom.col = "bin.chrom"
)
cnr |
a cnr bundle |
exclude.chr |
chromosomes to exclude, default X, Y |
monomorphic.threshold |
alteration frequency at which a locus is to be considered monomorphic (universally altered). default 0.95 |
noise.threshold |
lower-bound alteration frequency at which alterations are considered technical noise, rather than a true alteration, default 0.1 |
chrom.col |
name of column containing chromosomes |
Single-value with the proportion of polymorphic loci for a given sample population
data(cnr)
cnr <- get_alteration_frequencies(cnr)
proportion_of_polymorphic_loci(cnr)
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