Package: FamEvent 3.2

Yun-Hee Choi

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. For more information see Choi, Y.-H., Briollais, L., He, W. and Kopciuk, K. (2021) FamEvent: An R Package for Generating and Modeling Time-to-Event Data in Family Designs, Journal of Statistical Software 97 (7), 1-30.

Authors:Yun-Hee Choi, Karen Kopciuk, Wenqing He, Laurent Briollais

FamEvent_3.2.tar.gz
FamEvent_3.2.tar.gz(r-4.5-noble)FamEvent_3.2.tar.gz(r-4.4-noble)
FamEvent_3.2.tgz(r-4.4-emscripten)FamEvent_3.2.tgz(r-4.3-emscripten)
FamEvent.pdf |FamEvent.html✨
FamEvent/json (API)

# InstallFamEvent in R:
install.packages('FamEvent',repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • LSfam - Ontario Lynch Syndrom families

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

29 exports 0.09 score 16 dependencies 291 downloads

Last updated 3 days agofrom:8e0e70f0aa

Exports:carrierprobfampowerpenetrancepenetrance_cmppenmodelpenmodel_cmppenmodelEMpenplotpenplot_cmpplot.penmodelplot.penmodel_cmpplot.simfamplot.simfam_cmpplot.simfam_tvcplot.simfam2print.penmodelprint.penmodel_cmpprint.summary.penmodelprint.summary.penmodel_cmpsimfamsimfam_cmpsimfam_tvcsimfam2summary.penmodelsummary.penmodel_cmpsummary.simfamsummary.simfam_cmpsummary.simfam_tvcsummary.simfam2

Dependencies:cmprskehaevaluatehighrkinship2knitrlatticeMASSMatrixmatrixcalcpracmaquadprogsurvivaltruncnormxfunyaml

Readme and manuals

Help Manual

Help pageTopics
Family age-at-onset data simulation and penetrance estimationFamEvent-package
Compute mutation carrier probabilities for individuals with missing gentoypescarrierprob
Simulation-based power calculation for genetic effectfampower
Ontario Lynch Syndrom familiesLSfam
Penetrance function and confidence intervalspenetrance
Estimating Penetrances for competing risk models and confidence intervalspenetrance_cmp
Fit a penetrance modelpenmodel
Fit a penetrance model for competing risks datapenmodel_cmp
EM algorithm for estimating the penetrance model with missing genotypespenmodelEM
Plot penetrance functionspenplot
Plot penetrance functions from competing risk modelspenplot_cmp
Plot method for 'penmodel'plot.penmodel
Plot method for 'penmodel_cmp'plot.penmodel_cmp
Plot method for 'simfam' or Plot pedigreesplot.simfam
Plot method for 'simfam_cmp' or Plot pedigreesplot.simfam_cmp
Plot method for 'simfam_tvc' or Plot pedigreesplot.simfam_tvc
Plot method for 'simfam2' or Plot pedigreesplot.simfam2
Print method for 'penmodel'.print.penmodel
Print method for 'penmodel_cmp'.print.penmodel_cmp
Print method for 'summary.penmodel' of a fitted penetrance model.print.summary.penmodel
Print method for 'summary.penmodel_cmp' of a fitted competing risks penetrance model.print.summary.penmodel_cmp
Generate familial time-to-event datasimfam
Generate familial competing risks datasimfam_cmp
Generate familial time-to-event data with a time-varying covariatesimfam_tvc
Generate familial time-to-event data with Kinship or IBD matrices.simfam2
Summary method for class 'penmodel'summary.penmodel
Summary method for class 'penmodel_cmp'summary.penmodel_cmp
Summary method for 'simfam'summary.simfam
Summary method for 'simfam_cmp'summary.simfam_cmp
Summary method for 'simfam_tvc'summary.simfam_tvc
Summary method for 'simfam2'summary.simfam2