FamEvent is a comprehensive R package for simulating and modelling age-at-disease onset in families carrying a rare gene mutation. The package can simulate complex family data for variable time-to-event outcomes under three common family study designs (population, high-risk clinic and multi-stage) with various levels of missing genetic information among family members. Residual familial correlation can be induced through the inclusion of a frailty term or a second gene. Disease-gene carrier probabilities are evaluated assuming Mendelian transmission or empirically from the data. When genetic information on the disease gene is missing, an Expectation-Maximization algorithm is employed to calculate the carrier probabilities. Penetrance model functions with ascertainment correction adapted to the sampling design provide age-specific cumulative disease risks by sex, mutation status, and other covariates for simulated data as well as real data analysis. Robust standard errors and 95% confidence intervals are available for these estimates. Plots of pedigrees and penetrance functions based on the fitted model provide graphical displays to evaluate and summarize the models.
Keyphrases
- data analysis
- genome wide
- electronic health record
- copy number
- big data
- primary care
- machine learning
- emergency department
- oxidative stress
- preterm infants
- gene expression
- healthcare
- dna methylation
- metabolic syndrome
- adipose tissue
- deep learning
- health information
- genome wide identification
- early onset
- social media
- climate change
- human health
- quality improvement