ibdsegments (version 1.0.1)

r_cibd: Random generation for IBD on a continuous genome

Description

The r_cibd function generates random Identity-by-Descent (IBD) segments along a continuous genome, given a specified pedigree and observed individuals.

Usage

r_cibd(
  n,
  pedigree,
  ids = pedtools::leaves(pedigree),
  states = "ibd",
  ibd_state = 1L,
  chromosome_length = 267.77
)

Value

A list containing:

samples

Data frame of simulated IBD segments along the chromosome.

stats

Data frame with summary statistics per sample, including total IBD length and the segment count.

Arguments

n

Number of observations

pedigree

Pedigree in pedtools::ped form.

ids

Ids for which IBD is observed. Default is pedtools::leaves(pedigree).

states

One of "ibd (default), "kappa", "identity" or "detailed".

ibd_state

Default is 1.

chromosome_length

Default is 267.77 cM (an estimate of the length of chromosome 1).

Examples

## Basic example: IBD along one chromosome for half siblings
L <- 300
r_hs <- r_cibd(n = 1e4, pedigree = pedtools::halfSibPed(), chromosome_length = 300)

# half sibs alternate between IBD (state 1) and not IBD (state 0)
head(r_hs$samples)

# the total_length and number of segments per sample are also returned
head(r_hs$stats)

## Comparing half siblings and grandparent-grandchild
r_gp <- r_cibd(n = 1e4, pedigree = pedtools::linearPed(2), ids = c(1, 5),
               chromosome_length = 300)

hist(r_gp$stats$total_length)
hist(r_hs$stats$total_length)