Running TWINSIM

TWINSIM is a command driven program for simulating twin-nuclear families in which QTLs and linked markers are segregating.

Results of running the help command
MODEL SETTINGS
set mean <trait mean>
set prevalence <prev> [...<prevN>]
set va <additive variance> [vq [vc [ve]]]
set vc <shared environmental variance>
set ve <unshared environmental variance>
set vq <QTL additive variance>
set xlinked [on|off]
set pen <mu11> <mu12> <mu22> [<male_mu1> <male_mu2>]
set qtl <map position (cM)> [<increasing allele frequency> [<QTL additive variance>]]
set nqtl <no. of polygenes in finite polygenic model>
set map <marker map position 1 (cM)>...<marker map position N>
set nall <no. of marker alleles>|perfect
set fre <marker allele freq 1> <freq 2>...
set nfam <no. of nuclear families to be simulated>
set mzfam <no. of MZ families>
set halfsibs <no. of families with half-sibs>
set nsibs <no. of children per family>
SUMMARIZE MODEL
list|ls|show map
SIMULATION
set print 0|1|2
write loc <Sib-pair script> [<pedigree file name>]
simulate|write <pedigree file name> [nfam [nsibs [mzfam]]]
MISCELLANEOUS
set seeds <seed1> <seed2> <seed3>
set echo on|off
set prompt on|off
time
!|# <comment line>
%|$ <shell command to be run>
include <command file>
clear all settings
help
stop|quit

Results of running the help command
MODEL SETTINGS
set mean <trait mean>
set prevalence <prev> [...<prevN>]
set va <additive variance> [vq [vc [ve]]]
set vc <shared environmental variance>
set ve <unshared environmental variance>
set vq <QTL additive variance>
set xlinked [on\|off]
set pen <mu11> <mu12> <mu22> [<male_mu1> <male_mu2>]
set qtl <map position (cM)> [<increasing allele frequency> [<QTL additive variance>]]
set nqtl <no. of polygenes in finite polygenic model>
set map <marker map position 1 (cM)>...<marker map position N>
set nall <no. of marker alleles>\|perfect
set fre <marker allele freq 1> <freq 2>...
set nfam <no. of nuclear families to be simulated>
set mzfam <no. of MZ families>
set halfsibs <no. of families with half-sibs>
set nsibs <no. of children per family>
SUMMARIZE MODEL
list\|ls\|show map
SIMULATION
set print 0\|1\|2
write loc <Sib-pair script> [<pedigree file name>]
simulate\|write <pedigree file name> [nfam [nsibs [mzfam]]]
MISCELLANEOUS
set seeds <seed1> <seed2> <seed3>
set echo on\|off
set prompt on\|off
time
!\|# <comment line>
%\|$ <shell command to be run>
include <command file>
clear all settings
help
stop\|quit

Here is a simple job to produce a set of nuclear families of different size.

A sample job
# # SML (diallelic, P(A)=0.01) explaining 6% of variance located 40 cM # from map end. # Map comprises 9 markers: each has 6 alleles # with the specified frequencies. # set freq 0.1 0.5 0.2 0.1 0.05 0.05 set mean 1.43 set va 0 set map 5 20 31 50 60 61 80 90 98 set qtl 40 0.01 0.00178 set ve 0.027556 set mzfam 0 set nsibs 3 wri loc sim1.in sim.ped set nsibs 1 wri ped sim1.ped 100 set nsibs 2 wri ped sim2.ped 100 set nsibs 3 wri ped sim3.ped 50 $ cat sim1.ped sim2.ped sim3.ped > sim.ped

A sample job
# # SML (diallelic, P(A)=0.01) explaining 6% of variance located 40 cM # from map end. # Map comprises 9 markers: each has 6 alleles # with the specified frequencies. # set freq 0.1 0.5 0.2 0.1 0.05 0.05 set mean 1.43 set va 0 set map 5 20 31 50 60 61 80 90 98 set qtl 40 0.01 0.00178 set ve 0.027556 set mzfam 0 set nsibs 3 wri loc sim1.in sim.ped set nsibs 1 wri ped sim1.ped 100 set nsibs 2 wri ped sim2.ped 100 set nsibs 3 wri ped sim3.ped 50 $ cat sim1.ped sim2.ped sim3.ped > sim.ped

If "set prevalence" is issued, a multifactorial threshold model is fitted. When one or two proportions are given, the model includes one threshold and two categories. When more than two proportions are specified, there are N-1 thresholds in the usual ordinal fashion.

If the print level is set higher, the actual QTL genotypes will be included in the generated locus and pedigree file. For level 1, the first QTL is included, with level 2, the background QTL genotypes are added.