lrt_men_g4 {segtest} | R Documentation |
Likelihood ratio test for segregation distortion with known genotypes
Description
This will run a likelihood ratio test using the genotypes of an F1 population of tetraploids for the null of Mendelian segregation (accounting for double reduction and preferential pairing) against the alternative of segregation distortion. This is when the genotypes are assumed known.
Usage
lrt_men_g4(
x,
g1,
g2,
drbound = 1/6,
pp = TRUE,
dr = TRUE,
alpha = 0,
xi1 = 1/3,
xi2 = 1/3
)
Arguments
x |
A vector of genotype counts. |
g1 |
The genotype of parent 1. |
g2 |
The genotype of parent 2. |
drbound |
The maximum rate of double reduction. A default of 1/6 is provided, which is the rate under the complete equational segregation model of meiosis. |
pp |
A logical. Should we account for preferential pairing
( |
dr |
A logical. Should we account for double reduction
( |
alpha |
If |
xi1 |
If |
xi2 |
If |
Value
A list with the following elements
statistic
The log-likelihood ratio test statistic.
df
The degrees of freedom.
p_value
The p-value.
alpha
The estimated double reduction rate.
xi1
The estimated preferential pairing parameter of parent 1.
xi2
The estimated preferential pairing parameter of parent 2.
Impossible genotypes
Some offspring genotype combinations are impossible given the parental genotypes. If these impossible genotypes combinations show up, we return a p-value of 0, a log-likelihood ratio statistic of Infinity, and missing values for all other return items. The impossible genotypes are:
g1 = 0 && g2 = 0
Only offspring genotypes of 0 are possible.
g1 = 4 && g2 = 4
Only offspring genotypes of 4 are possible.
g1 = 0 && g2 = 4 || g1 == 4 && g2 == 0
Only offspring genotypes of 2 are possible.
g1 = 0 && g2 %in% c(1, 2, 3) || g1 = %in% c(1, 2, 3) && g2 == 0
Only offspring genotypes of 0, 1, and 2 are possible.
g1 = 4 && g2 %in% c(1, 2, 3) || g1 = %in% c(1, 2, 3) && g2 == 4
Only offspring genotypes of 2, 3, and 4 are possible.
Unidentified parameters
When g1 = 2
or g2 = 2
(or both), the model is not identified
and those estimates (alpha
, xi1
, and xi2
) are
meaningless. Do NOT interpret them.
The estimate of alpha
(double reduction rate) IS identified as
long as at least one parent is simplex, and no parent is duplex.
However, the estimates of the double reduction rate have extremely high
variance.
Author(s)
David Gerard
Examples
set.seed(100)
gf <- offspring_gf_2(alpha = 1/12, xi1 = 0.2, xi2 = 0.6, p1 = 1, p2 = 0)
x <- offspring_geno(gf = gf, n = 100)
lrt_men_g4(x = x, g1 = 1, g2 = 0)