Description Usage Arguments Value References Examples
For each methylation site, this function computes certain maximum likelihood estimates and a measure of heritability called Δl (with higher values corresponding to more highly heritable methylation sites), as described briefly below and fully in (Joo et al., 2018).
1 | ML_estimates(typed_genos, M_values, sort = TRUE, na_omit = TRUE, ncores = 1)
|
typed_genos |
A named list, usually generated by
|
M_values |
A matrix of M-values,with rows corresponding to the
methylation sites and columns corresponding to people.
The column names should correspond to the column names appearing in
|
sort |
Re-order the methylation sites to have decreasing values of |
na_omit |
Remove any methylation sites with missing values ( |
ncores |
The number of cores to be used, with |
A data frame with 15 columns. In the column names, the suffixes
.mendel
and .mix
refer the Mendelian and mixture models of
(Joo et al., 2018).
Briefly, the mixture model is the standard Gaussian mixture model with two
groups (group 0
and group 1
),
so group memberships are independent and the M-values of each group are
normally distributed. The Mendelian model is the same except that group
memberships are dependent within families, and are modelled as the carrier
status of a rare, autosomal genetic variant.
In the column names, the prefixes mu
and sd
refer to the maximum
likelihood estimates of the mean and standard deviation of each group's
normal distribution, and the suffix ll
refers to each model's maximised
log-likelihood (i.e., the log-likelihood function evaluated at the maximum
likelihood estimates). The suffix .null
refers to the null model that is
nested inside both the Mendelian and mixture models, in which the means and
standard deviations for the two groups are equal
(i.e., mu0 = mu1
and sd0 = sd1
).
The column delta.l
gives the difference between ll.mendel
and ll.mix
,
and is the measure of heritability (Δl) that was introduced in
(Joo et al., 2018).
Joo JE, Dowty JG, Milne RL, Wong EM, Dugué PA, English D, Hopper JL, Goldgar DE, Giles GG, Southey MC, kConFab. Heritable DNA methylation marks associated with susceptibility to breast cancer. Nat Commun. 2018 Feb 28;9(1):867. https://doi.org/10.1038/s41467-018-03058-6
1 2 3 4 5 6 7 8 9 10 11 12 | # Example data
str(ped)
str(M_values)
# Calculate genotype probabilities
typed_genos <- genotype_combinations(ped)
str(typed_genos)
# Compute Delta l
MLEs <- ML_estimates(typed_genos, M_values, ncores = 4)
str(MLEs)
|
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