This package implements regression models for family-based genetic studies, including mixed models. While such models can be fit with other existing software, this package tries to provide a unified solution that leverages the flexibility of the R environment. It also leverages modern automatic differentiation techniques to fit likelihood-based models quickly.
Installation
You can install the latest released version of FamModel from GitHub with:
# install.packages("devtools")
devtools::install_github("kinnamon-lab/FamModel", ref = "[tag]")where [tag] is the tag of the most recent release.
Example
The following code fits a univariate version of the linear mixed model presented in Cowan et al. (2018) with an equivalent parameterization using the lmna_nonseg example data provided with the package. Note how the package permits flexible use of formula constructs and provides an appropriate likelihood ratio test for a null narrow-sense heritability on the boundary of the parameter space.
lmna_data <- copy(lmna_nonseg)[,
`:=`(
female = as.integer(sex == 2),
# Use N rather than N-1 for SD divisor in standardization (like Mendel 16.0)
age_echo_std = (age_echo_yrs - mean(age_echo_yrs, na.rm = TRUE)) /
(
sd(age_echo_yrs, na.rm = TRUE) *
sqrt((sum(!is.na(age_echo_yrs)) - 1) / sum(!is.na(age_echo_yrs)))
)
)
]
lmna_fd <- FamData$new(
lmna_data,
family_id = "family_ID",
indiv_id = "individual_ID",
proband = "proband",
sex = "sex",
maternal_id = "maternal_ID",
paternal_id = "paternal_ID",
mzgrp = "mzpair",
dzgrp = "dzpair"
)
lmna_lvef_model <- lmna_fd$lmm(
lvef ~ female + age_echo_std + I(n_lmna_vars > 0) + I(n_oth_vars > 0)
)
lmna_lvef_model$print()===LINEAR MIXED MODEL RESULTS===
DATA: lmna_data
MEAN MODEL: lvef ~ female + age_echo_std + I(n_lmna_vars > 0) + I(n_oth_vars >
0)
VARIANCE PARAMETER GROUPS: ~1
FAMILIES USED: 5
SUBJECTS USED: 36
PROBANDS: 5
FAMILY SIZE DISTRIBUTION:
2 4 7 19
1 2 1 1
CONVERGENCE ACHIEVED AT -2 LL = 251.2582
EVALUATIONS:
function gradient
22 22
MESSAGE: CONVERGENCE: NORM OF PROJECTED GRADIENT <= PGTOL
MAX ABSOLUTE ELEMENT OF LL GRADIENT (g) AT SOLUTION: 2.111349e-06
NEGATIVE LL HESSIAN (-H) CHARACTERISTICS AT SOLUTION:
SMALLEST EIGENVALUE: 2.071621e-02
RECIPROCAL CONDITION NUMBER: 2.204742e-03
SCALED LL GRADIENT (-g' * H^-1 * g) CRITERION AT SOLUTION: 5.399669e-12
VARIANCE PARAMETERS
Parameter Estimates
-------------------
Estimate SE
h2_a 0.35479 0.59385
sigma 14.23753 2.05032
Likelihood Ratio Tests
----------------------
Ho Max |g| -g' * H^-1 * g Min lambda(-H) 1 / kappa(-H) LR X^2 Pr(> X^2)
h2_a = 0 1.788213e-08 1.015742e-15 2.038201e-02 6.474284e-02 0.48601 0.24286
MEAN MODEL
Parameter Estimates
-------------------
Estimate SE 95% LCL 95% UCL Z value Pr(>|Z|)
(Intercept) 50.6429 5.9038 39.0717 62.2142 8.5780 < 2.2e-16 ***
female 3.4080 5.2904 -6.9609 13.7770 0.6442 0.519446
age_echo_std -5.6955 3.1419 -11.8535 0.4626 -1.8127 0.069873 .
I(n_lmna_vars > 0)TRUE 3.3815 5.7393 -7.8674 14.6303 0.5892 0.555747
I(n_oth_vars > 0)TRUE -13.3117 5.1573 -23.4199 -3.2035 -2.5811 0.009848 **
---
Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
NOTE: Wald tests and CIs are displayed in the above outputAcknowledgements
Development of this software was supported by the National Heart, Lung, and Blood Institute and National Human Genome Research Institute of the National Institutes of Health under award numbers R01HL128857 and R01HL149423. The content is solely the responsibility of the author and does not necessarily represent the official views of the National Institutes of Health.
