FamEvent: Family Age-at-Onset Data Simulation and Penetrance Estimation

Simulates age-at-onset traits associated with a segregating major gene in family data obtained from population-based, clinic-based, or multi-stage designs. Appropriate ascertainment correction is utilized to estimate age-dependent penetrance functions either parametrically from the fitted model or nonparametrically from the data. The Expectation and Maximization algorithm can infer missing genotypes and carrier probabilities estimated from family's genotype and phenotype information or from a fitted model. Plot functions include pedigrees of simulated families and predicted penetrance curves based on specified parameter values.

Author
Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais
Date of publication
2016-09-30 22:58:33
Maintainer
Yun-Hee Choi <yun-hee.choi@schulich.uwo.ca>
License
GPL (>= 2.0)
Version
1.2

View on CRAN

Man pages

carrierprob
Compute mutation carrier probabilities for individuals with...
FamEvent-package
Family age-at-onset data simulation and penetrance estimation
penmodel
Estimate the penetrance model and penetrance curves
penmodelEM
EM algorithm for estimating the penetrance model with missing...
penplot
Plot the penetrance function
plot.penmodel
Plot estimated penetrance curves from a model fit
plot.simfam
Plot pedigrees
simfam
Generate familial time-to-event data
summary.penmodel
Summary of a penetrance model fit
summary.simfam
Summary of simulated data

Files in this package

FamEvent
FamEvent/NAMESPACE
FamEvent/R
FamEvent/R/kids.g.R
FamEvent/R/hazards.R
FamEvent/R/inv.survp.R
FamEvent/R/pen.ci.R
FamEvent/R/surv.dist.R
FamEvent/R/simfam.R
FamEvent/R/inv.surv.R
FamEvent/R/plot.simfam.R
FamEvent/R/penfrailtymodel.R
FamEvent/R/floglik.vec.R
FamEvent/R/carrierprobgeno.R
FamEvent/R/penf.R
FamEvent/R/familyStructure.R
FamEvent/R/loglik.R
FamEvent/R/floglik.R
FamEvent/R/summary.simfam.R
FamEvent/R/loglikem.R
FamEvent/R/Pgene.R
FamEvent/R/laplace.R
FamEvent/R/floglikem.R
FamEvent/R/survp.dist.R
FamEvent/R/carrierprobpheno.R
FamEvent/R/numericGradient.R
FamEvent/R/plot.penmodel.R
FamEvent/R/fgene.R
FamEvent/R/gh.R
FamEvent/R/parents.g.R
FamEvent/R/penmodelEM.R
FamEvent/R/carrierprob.R
FamEvent/R/cumhaz.R
FamEvent/R/summary.penmodel.R
FamEvent/R/penplot.R
FamEvent/R/penmodel.R
FamEvent/R/FamilyData-internal.R
FamEvent/R/loglik.vec.R
FamEvent/R/cprob.frailty.R
FamEvent/R/cprob.R
FamEvent/R/familydesign.r
FamEvent/R/dlaplace.R
FamEvent/MD5
FamEvent/DESCRIPTION
FamEvent/man
FamEvent/man/FamEvent-package.Rd
FamEvent/man/summary.penmodel.Rd
FamEvent/man/plot.penmodel.Rd
FamEvent/man/carrierprob.Rd
FamEvent/man/penmodelEM.Rd
FamEvent/man/summary.simfam.Rd
FamEvent/man/simfam.Rd
FamEvent/man/penmodel.Rd
FamEvent/man/plot.simfam.Rd
FamEvent/man/penplot.Rd