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simulation of consanguineous unions in human populations with R

2 messages · Hinda Haned, Thibaut Jombart

Original
Hinda Haned
# 
Dear list members,

I was wondering if anyone had experience simulating non-random mating 
human populations with R.

I want  to simulate the evolution of disease susceptibility loci under certain evolutionary scenarios and under specific non-random mating schemes. 
For example, at each generation, p% of the matings occur between first cousins, offspring from such unions (must) have on average 
1/16 of their genome autozygous.
I've been  exploring  simulation softwares  for a while , but they  offer limited  mating schemes, mainly because relationships between individuals can not be extracted.
Any ideas or suggestions are welcome !
Thank you .
2 days later
Thibaut Jombart
#
Hinda Haned wrote:
Hi Hinda,

I don't know how advanced the tools for simulating genetic data are in 
R. Maybe we are not very far, or not that far yet. The package rmetasim 
is said to perform individual-based population genetics simulation, so 
it may be worth having a look there:
http://cran.r-project.org/web/packages/rmetasim/index.html

Otherwise, there is a package GeneticsPed in the Rgenetics project for 
handling pedigree data:
http://bioconductor.org/packages/devel/bioc/html/GeneticsPed.html

but it seems to be in an early stage of development, and it does not 
seem to perform data simulations.

Good luck,

Thibaut.