reassign_gen: Reassign generation number based on affected status

In SimRVPedigree: Simulate Pedigrees Ascertained for a Rare Disease

Description

The reassign_gen function assigns generation numbers among affected family members so that generation 1 represents the most recent generation that a putative disease variant shared identical by descent (IBD), as defined in Thompson (2000), by affected members could have been introduced into the pedigree.

Usage

reassign_gen(ped_file)

Arguments

ped_file

An object of class ped. A pedigree generated by sim_ped or sim_RVped, or an object created by the function new.ped. See details.

Details

**reassign_gen cannot be applied to pedigrees that contain loops or inbreeding.**

The reassign_gen function accepts a pedigree and reassigns generation numbers among disease-affected relatives so that generation 1 represents the generation of the most recent common ancestor of all disease-affected relatives. We note that the individual in generation 1 could themselves be disease-affected, i.e. an individual can be considered their own ancestor.

For example, consider a family with 2 affected members. If the disease-affected relatives are a parent and a child, the affected parent would be assigned generation 1, and the affected child generation 2. However, if the disease-affected relatives are a pair of siblings, each is be assigned generation 2 since a common parent of the two is assumed to be a carrier of a latent susceptibility variant. Similarly, if the disease-affected relatives are a pair of cousins, is assigned generation 3, since a common grandparent is the most recent common ancestor from whom they could have inherited a shared variant associated with the disease.

Users who wish to assign generation number based on affection status in pedigrees that have not been simulated with the SimRVpedigree package must create a ped object using new.ped.

Value

A ped object containing only affected members, obligate carriers, and founders with generation numbers reassigned among disease-affected relatives based on their most recent common ancestor, as described in details.

References

Nieuwoudt, Christina and Jones, Samantha J and Brooks-Wilson, Angela and Graham, Jinko (2018). Simulating Pedigrees Ascertained for Multiple Disease-Affected Relatives. Source Code for Biology and Medicine, 13:2.

Thompson, E. (2000). Statistical Inference from Genetic Data on Pedigrees. NSF-CBMS Regional Conference Series in Probability and Statistics, 6, I-169.

See Also

new.ped

Examples

# Read in example pedigrees
data(EgPeds)
class(EgPeds)

# Create ped object
Bpeds <- new.ped(EgPeds)
summary(Bpeds)

# Reassign generation numbers in the first four pedigrees in EgPeds
Apeds <- lapply(seq_len(5), function(x){
                 reassign_gen(Bpeds[Bpeds$FamID == x, ])})
Apeds <- do.call(rbind, Apeds)

# Compare pedigrees before and after reassigning
# generation number based on affected status
par(mfrow = c(1, 2))
for (k in 1:5) {
  plot(subset(Bpeds, FamID == k), gen_lab = TRUE, plot_legend = FALSE)
  mtext(paste0("Ped", k, ": before generation reassignment", sep = ""),
        side = 3, line = 1.5)

  plot(subset(Apeds, FamID == k), gen_lab = TRUE, plot_legend = FALSE)
  mtext(paste0("Ped", k, ": after generation reassignment", sep = ""),
        side = 3, line = 1.5)
}
par(mfrow = c(1, 1))

SimRVPedigree documentation built on Feb. 10, 2020, 1:07 a.m.