po_gl {segtest} | R Documentation |
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. |
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)
[Package segtest version 2.0.0 Index]