LOD scores indicate the log ratio of the likelihood of the marker data at this position with the MLE estimate of the sibling recurrence risk ratio, versus the likelihood assuming a sibling risk ratio of 1. Empirical genome-wide p values were calculated via simulation.
Measures below the LOD were assigned values using maximum likelihood, assuming a log-normal distribution (El-Shaarawi and Viveros 1997).
This is typically done by maximizing the likelihood assuming a simple parametric model for the population size change.
The InVEst method estimates the parameters of kinetic rate Eq. (2) using maximum likelihood, assuming relative error in all measurements.
Estimation of the parameters was carried out by the method of maximum likelihood, assuming normal distributions for the outcome variables.
The PCGs of the 21 mitogenomes were used to estimate dN/dS ratios (the ω parameter) by maximum likelihood, assuming rate constancy per codon site and branch.
Profile likelihoods were estimated through the MCMC search of the parameter space, and confidence intervals were calculated from the profile likelihood, assuming the likelihood surface was approximately chi-squared distributed [ 26].
VARiD can use both of these sources of information, either converting a quality value into an error likelihood (assuming it is on the standard Phred scale) or using pre-specified error likelihoods for every position in a read.
This likelihood assumes that dropout at a locus is independent across individuals, so that each observed diploid genotype of an individual at the locus is a separate trial independent of all others.
(1) Normalized Site Likelihood Ratio (NSLR ): this feature attempts to capture the tree-like signal in a site by comparing its likelihood assuming a reasonable tree topology (log(l i )) and the star tree (log(r i )) with infinite edge lengths.
Figure 1 shows LRTlin-con,ϕ against ϕ for these two cancers, while Figure 2 shows the fitted values ERR1 = when ϕ ≥ 30 with 95%CIs (Profile Likelihood, assuming LRT ~ χ2 on 1 d.f. for testing β = β0 against β ≠ β0).
