segtest (version 2.0.0)

po_gl: 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
)

Value

Genotype likelihoods

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.

Author

Mira Thakkar

Examples

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