proportion_of_polymorphic_loci: proportion of polymorphic alleles as subclonal

View source: R/genetic_diversity.R

proportion_of_polymorphic_lociR Documentation

proportion of polymorphic alleles as subclonal

Description

Estimate genome-wide proportion of polymorphic loci in a population

Usage

proportion_of_polymorphic_loci(
  cnr,
  exclude.chr = c("X", "Y"),
  monomorphic.threshold = 0.95,
  noise.threshold = 0.1,
  chrom.col = "bin.chrom"
)

Arguments

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

Value

Single-value with the proportion of polymorphic loci for a given sample population

Examples

data(cnr)

cnr <- get_alteration_frequencies(cnr)

proportion_of_polymorphic_loci(cnr)


SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.