alleleSummary: Allele sharing summary

Description

This function summarises the allele flow for selected individuals, for a single genome simulation.

Usage

alleleSummary(x, ids, ibd.status = FALSE)

Arguments

A single genome simulation, i.e. a list of simulated chromosomes. Each chromosome is a list, with one entry for each individual. Each of these entries is a list of two matrices (one for each strand). The matrices have 2 columns (start position; allele) and one row for each segment unbroken by recombination.

ids

A vector of numerical IDs. If missing, all individuals are included.

ibd.status

A logical, meaningful only if length(ids)==2. If TRUE the IBD status (number of alleles shared IBD, either 0 1 or 2) of each segment is computed, as well as the breakdown of their parental origin.

Value

A numerical matrix. Each row corresponds to a chromosomal segment. The first 4 columns describe the segment (chromosome, start, end, length), and are followed by two columns (paternal allele, maternal allele) for each of the selected individuals. If ibd.status=TRUE five more columns are added: ibd, ibd_pp, ibd_pm, ibd_mp and ibd_mm. The first of these indicate the IBD status (0, 1 or 2) in the segment, while the latter 4 give the parental breakdown of this number. For instance, ibd_pm is 1 if the _p_aternal allele of the first individual is IBD with the _m_aternal allele of the second individual, and 0 otherwise.

Details

This function is useful for downstream analysis of simulations produced by IBDsim.

Examples

Run this code

# NOT RUN {
### Sibling simulation (3 sims of chromosomes 1 and 2)
x = nuclearPed(2)
sim = IBDsim(x, sims=3, chromosomes=1:2)

alleleSummary(sim[[1]]) # First sim, summary of all individuals
alleleSummary(sim[[1]], ids=3:4) # Summary of the siblings
alleleSummary(sim[[1]], ids=3:4, ibd.status=TRUE) # IBD breakdown of the siblings

# Trivial example: Summary of the father.
# Being the first founder, his alleles are denoted 1 and 2 everywhere.
fa = alleleSummary(sim[[1]], ids=1) 
stopifnot(all(fa[,c('1p', '1m')]==c(1,1,2,2)))

# }