Class | Analysis and data manipulation command |
Name | simulate |
Arguments | <trait> [<h2> [<linked extant marker>]] |
The data for the named trait is replaced by simulated data for a trait under the control of a QTL (or polygenes) with a total heritability of h2 (defaulting to 50%). If a second marker name is given, the controlling QTL is simulated as being completely linked to the second marker.
Example:
>> include longqtex.in >> set locus qtrait quantitative >> set seeds 1 1 1 >> simulate qtrait >> varcomp qtrait ------------------------------------------------ Variance components analysis for "qtrait" ------------------------------------------------ Random: A+D Number of families = 1 Number of MZ twinships = 0 Number of observations = 73 Trait mean (intercept) = -0.181935 Additive genetic variance = 0.932705 ( 68.4%) 95% Profile likelihood CI = 0.374085 -- 1.232237 Environmental variance = 0.431475 ( 31.6%) Model loglikelihood = -38.645440 Chi-square testing VD=0 = -0.00 (df=1, P=0.500) Chi-square testing VG=0 = 9.00 (df=1, P=0.003)
Class | Analysis and data manipulation command |
Name | simulate |
Arguments | <marker> [<linked extant marker>] [<number of equifrequent marker alleles> | <allele 1 frequency>...<allele N frequency>]. |
The data for the named autosomal marker is replaced by simulated data. If a second marker name is given, the new marker is simulated as being completely linked to the second marker. Either a set of allele frequencies, or the number of (equifrequent) alleles, can be given for the simulation. If the sum of the given allele frequencies is less than 1, an extra allele will be added automatically.
Example:
>> include longqtex.in >> set loc m2 marker >> sim m2 marker 4 Simulating "m2" as a 4-allele marker linked to "marker". >> lin --------------------------------------------------- Inter-marker sib pair linkage analysis --------------------------------------------------- Marker 1 Marker 2 Sibships Sibpairs r(IBD) Recomb -------------- -------------- -------- -------- ------ ------- marker m2 14 155 0.990 0.003 0.002--0.004
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