po_gl: Generate genotype likelihoods from offspring genotypes.

In segtest: Tests for Segregation Distortion in Polyploids

Generate genotype likelihoods from offspring genotypes.

Description

Takes as input (i) the parent genotypes, (ii) the offspring genotype frequency, (iii) sequencing error rate, (iv) read depth, (v) bias, and (vi) overdispersion. It returns genotype likelihoods.

Usage

po_gl(
  genovec,
  ploidy,
  p1_geno = NULL,
  p2_geno = NULL,
  rd = 10,
  seq = 0.01,
  bias = 1,
  od = 0.01
)

Arguments

genovec	Offspring genotypes. genovec[i] is the dosage for individual i.
ploidy	Ploidy
p1_geno	Parent 1 genotype
p2_geno	Parent 2 genotype
rd	Read depth. Lower is more uncertain.
seq	Sequencing error rate. Higher means more uncertain.
bias	Bias. 1 means no bias.
od	Overdispersion. Typical value is like 0.01. Higher means more uncertain.

Value

Genotype likelihoods

Author(s)

Mira Thakkar

Examples

set.seed(1)
po_gl(genovec = c(1, 2, 1, 1, 3), p1_geno = 2, p2_geno = 2, ploidy = 4)

segtest documentation built on July 1, 2025, 1:07 a.m.