FamEvent: Family Age-at-Onset Data Simulation and Penetrance Estimation
Version 1.3

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.

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AuthorYun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais
Date of publication2017-03-26 07:30:45 UTC
MaintainerYun-Hee Choi <yun-hee.choi@schulich.uwo.ca>
LicenseGPL (>= 2.0)
Version1.3
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("FamEvent")

Man pages

carrierprob: Compute mutation carrier probabilities for individuals with...
FamEvent-package: Family age-at-onset data simulation and penetrance estimation
penci: Estimate the confidence intervals for the penetrances
penf: Penetrance function
penmodel: Estimate the penetrance model and penetrance curves
penmodelEM: EM algorithm for estimating the penetrance model with missing...
penplot: Plot penetrance functions
plot.penmodel: Plot method for 'penmodel'
plot.simfam: Plot method for 'simfam' or Plot pedigrees
print.penmodel: Print method for 'penmodel'.
print.summary.penmodel: Print method for 'summary.penmodel' of a fitted penetrance...
simfam: Generate familial time-to-event data
summary.penmodel: Summary method for class 'penmodel'
summary.simfam: Summary method for 'simfam'

Functions

FamEvent-package Man page
Pgene Source code
carrierprob Man page Source code
carrierprobgeno Source code
carrierprobpheno Source code
cprob Source code
cprob.frailty Source code
cumhaz Source code
dlaplace Source code
familyDesign Source code
familyStructure Source code
fgene Source code
floglik Source code
floglik.vec Source code
floglikem Source code
gh Source code
hazards Source code
inv.surv Source code
inv.survp Source code
kids.g Source code
laplace Source code
loglik Source code
loglik.vec Source code
loglikem Source code
numericGradient Source code
parents.g Source code
pen.ci Source code
penci Man page Source code
penf Man page Source code
penfrailtymodel Source code
penmodel Man page Source code
penmodelEM Man page Source code
penplot Man page Source code
plot.penmodel Man page Source code
plot.simfam Man page Source code
print.penmodel Man page Source code
print.summary.penmodel Man page Source code
simfam Man page Source code
summary.penmodel Man page Source code
summary.simfam Man page Source code
surv.dist Source code
survp.dist Source code

Files

NAMESPACE
R
R/kids.g.R
R/hazards.R
R/inv.survp.R
R/pen.ci.R
R/surv.dist.R
R/simfam.R
R/inv.surv.R
R/plot.simfam.R
R/penfrailtymodel.R
R/floglik.vec.R
R/carrierprobgeno.R
R/penf.R
R/familyStructure.R
R/loglik.R
R/floglik.R
R/summary.simfam.R
R/loglikem.R
R/Pgene.R
R/laplace.R
R/floglikem.R
R/print.summary.penmodel.R
R/survp.dist.R
R/carrierprobpheno.R
R/numericGradient.R
R/plot.penmodel.R
R/fgene.R
R/gh.R
R/parents.g.R
R/penmodelEM.R
R/carrierprob.R
R/cumhaz.R
R/summary.penmodel.R
R/penplot.R
R/penmodel.R
R/FamilyData-internal.R
R/loglik.vec.R
R/cprob.frailty.R
R/print.penmodel.R
R/penci.R
R/cprob.R
R/familydesign.r
R/dlaplace.R
MD5
DESCRIPTION
man
man/print.penmodel.Rd
man/FamEvent-package.Rd
man/summary.penmodel.Rd
man/plot.penmodel.Rd
man/penf.Rd
man/print.summary.penmodel.Rd
man/carrierprob.Rd
man/penmodelEM.Rd
man/summary.simfam.Rd
man/simfam.Rd
man/penmodel.Rd
man/plot.simfam.Rd
man/penci.Rd
man/penplot.Rd
FamEvent documentation built on May 20, 2017, 5:39 a.m.