GenerateIndexPedigree: GenerateIndexPedigree

In GenerateIndexPedigree: Generate Pedigrees for Index Case Based on US Census Data

GenerateIndexPedigree

Description

Function to simulate pedigree of index case to first cousins and back to grandparents; Genetic mutation of index is permeated through pedigree, and if the family members are told about mutation and if they uptake genetic testing is tracked

Usage

GenerateIndexPedigree(
  age,
  sex,
  keep_future_children = TRUE,
  variant = "None",
  denovo_rate = 2e-06,
  is_denovo = NA,
  tell_family_prob = 0.7,
  tell_children_prob = 0.8,
  uptake_test_prob = 0.45,
  verbose = FALSE
)

Arguments

age	numeric, age of index case
sex	character, index case sex; either "M" or "F"
keep_future_children	logical, whether to keep (TRUE) or remove (FALSE) children not yet born; default is TRUE
variant	character, name of variant; default is "None" for unaffected index
denovo_rate	numeric, between 0 and 1; rate of denovo mutation in given variant; default is 1/500000 or 2x10^(-6)
is_denovo	logical, index mutation is de novo (TRUE) or inherited (FALSE); NA indicates denovo status is unknown and will be simulated; default is NA
tell_family_prob	numeric, between 0 and 1; probability that an index case tells their family about their mutation; default is 0.70
tell_children_prob	numeric, between 0 and 1; probability that an index case tells their children about their mutation, assumed this is <= tell_family_prob; default is 0.80
uptake_test_prob	numeric, between 0 and 1; probability that a family member who is told about index mutation will get a genetic test; default is 0.45
verbose	logical, whether to print messages during function; default is FALSE

Details

This function simulates pedigrees of individuals with a genetic mutation of interest, tracking family structure, variant permeation, and uptake of genetic testing. Family sizes are based on appropriate US census data, and due to correlation between number of children within pedigrees, this starts with assigning overall pedigree size to small, average, or large.

Children for each adult are generated using the SimulateChildren function.

Value

a data frame representing the family, where each row represents a person and columns represent attributes:

Age

numeric, person age

Sex

character, person sex; either "M" or "F"

RelationshipToIndex

character, person's relationship to index

ChildOf

character, which family member person is child of; NA for grandparents

DeNovo

logical, NA/True whether mutation is de novo; only possible to be true for index and parent

Variant

character, person's variant status; either NA or same as parameter

Told

character, Yes/No, whether person was informed of index case

UptakeTesting

character, Yes/No, on whether person chose to receive genetic health screening

Author(s)

Katelyn Queen [e-mail]

References

Schweizer and Guzzo. Distributions of Age at First Birth, 1960-2018 (2020); https://www.bgsu.edu/ncfmr/resources/data/family-profiles/schweizer-guzzo-distribution-age-first-birth-fp-20-11.html

Khandwala, Zhang, Lu, and Eisenberg. The age of fathers in the USA is rising: an analysis of 168 867 480 births from 1972 to 2015, Human Reproduction, Volume 32, Issue 10, October 2017, Pages 2110–2116, https://doi.org/10.1093/humrep/dex267

Examples

GenerateIndexPedigree(age = 35, variant = "BRCA1", sex = "M", is_denovo = NA)

GenerateIndexPedigree documentation built on June 17, 2026, 1:08 a.m.