This package provides functions to generate time-to-event data in the context of familial studies and to fit familial time-to-event data by correcting for ascertainment bias arising from a specified study design based on probands' mutation and disease statuses. The options on study designs are: "pop" for population-based design where families are ascertained through affected probands, "pop+" for population-based design with affected and mutation carrier probands, "cli" for clinic-based design that includes affected probands with at least one parent and one sib affected, "cli+" for clinic-based design that includes affected and mutation carrier probands with at least one parent and one sib affected, and "twostage" for two-stage design that randomly samples families from the population in the first stage and oversamples high risk families that include at least two affected members in the family in the second stage.
● Data Source:
CranContrib
● Keywords: package
● Alias: FamEvent-package
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Summary method for penmodel. Provides summary of a penetrance model fit including model parameter and penetrance estimates.
● Data Source:
CranContrib
● Keywords: summary
● Alias: summary.penmodel
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This function computes carrier probabilities for individuals with missing genotypes conditional on observed mutation in the family members. The alternative approach, carrierprobpheno, uses both observed mutation and phenotype information among family members.
● Data Source:
CranContrib
● Keywords: Carrier probability
● Alias: carrierprobgeno
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Plot method for penmodel. Plots penetrance curves estimated from the model fit and overlays non-parametric penetrance curves estimated from the data without proabands.
● Data Source:
CranContrib
● Keywords: Penetrance
● Alias: plot.penmodel
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This function computes model-based carrier probabilities for individuals with missing genotypes based on observed pheotypes and mutation status of family members using the fitted penetrance model.
● Data Source:
CranContrib
● Keywords: Carrier probability
● Alias: carrierprobpheno
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penmodelEM
(Package: FamEvent) :
EM algorithm for estimating the penetrance model with missing genotypes
This function fits family data with missing genotypes via the EM algorithm and provides model parameter estimates and corresponding gender- and genotype-specific penetrance estimates.
● Data Source:
CranContrib
● Keywords: Penetrance
● Alias: penmodelEM
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Summary method for simfam. Provides summaries of simulated data.
● Data Source:
CranContrib
● Keywords: summary
● Alias: summary.simfam
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This function generates familial time-to-event data for specified study design, genetic model and source of residual familial correlation; the generated data frame also contains family structure (individual's id, father id, mother id, relationship to proband, generation), gender, current age, genotypes of major or second genes.
● Data Source:
CranContrib
● Keywords: Simulation
● Alias: simfam
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penmodel
(Package: FamEvent) :
Estimate the penetrance model and penetrance curves
This function fits the penetrance model to the family data based on a prospective likelihood with ascertainment correction and provides parameter estimates as well as the gender- and mutation-specific penetrance estimates.
● Data Source:
CranContrib
● Keywords: Penetrance
● Alias: penmodel
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1 images
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Plot method for simfam. Provides pedigree plots for specified families generated from simfam function with option to save plots into a pdf file.
● Data Source:
CranContrib
● Keywords: Pedigree plot
● Alias: plot.simfam
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