Class | Global Utility |
Name | sml |
Arguments | <Frequency of A allele> <Penetrance of AA genotype> <Penetrance of AB genotype> <Penetrance of BB genotype> |
Calculates recurrence risks and segregation ratios under a specified diallelic generalized single major locus model.
The results include the input penetrances, the resulting trait prevalence, the population attributable risk fraction ("Pop AR"):
AR = (Prev-min(fAA,fAB,fBB))/Prev ;
the additive and dominance variances following James [1971], the expected recurrence risks, relative risks, odds ratios and population risk ratios for four classes of relative pair (MZ twins, full siblings, parent-offspring pairs, second degree relatives):
Rec Riski = Pr(Ego affected | relative of ith class affected)
Rel Riski = Pr(Ego affected | relative of ith class affected)
/ Pr(Ego affected | relative of ith class unaffected)
Odds Ratioi = Odds(Ego affected | relative of ith class affected)
/ Odds(Ego affected | relative of ith class unaffected)
PRRi = Pr(Ego affected | relative of ith class affected) / Prevalence ;
the expected identity-by-descent sharing for those four types of pair at the trait locus for concordantly affected and discordant pairs; the allele and genotype frequencies in affected and unaffected individuals; the risk to offspring by mating type (zero, one or both parents affected).
Example:
>> sml 0.17 0.21 0.08 0.03 ------------------------------------------------ Single Major Locus Recurrence Risk Calculation ------------------------------------------------ Frequency(A): 0.170000; Pen(AA): 0.210; Pen(AB): 0.080; Pen(BB): 0.030 Trait Prev : 0.049312; Pop AR: 39.2%; Var(Add): 0.001141; Var(Dom): 0.000127 Measure MZ Twin Sib-Sib Par-Off Second ---------- ---------- ---------- --------- ---------- Rec risk 0.075 0.062 0.061 0.055 Rel risk 1.564 1.264 1.250 1.124 Odds rat 1.610 1.281 1.266 1.131 PRR 1.522 1.248 1.235 1.117 ibd|A-A 1.000 0.552 0.500 0.276 ibd|A-U 1.000 0.497 0.500 0.248 Freq of A if Affected: 0.351983 (0.123,0.458,0.419) Freq of A if Unaffctd: 0.160561 (0.024,0.273,0.703) Mating Proportion Risk to offspring ---------- ----------- ------------------ UnA x UnA 0.904 0.048 Aff x UnA 0.094 0.060 Aff x Aff 0.002 0.075
See also:
grr | recurrence risks |
Class | Global Utility |
Name | sml |
Arguments | <Frequency of A allele> <Mean for AA genotype> <Mean for AB genotype> <Mean for BB genotype> <standard deviation for AA genotype>[<AB SD> [<BB SD>]]. |
Calculates mean, variance components and parent-offspring regression results under a specified diallelic generalized single major locus model.
Example:
>> sml 0.05 5 0 -5 1 ------------------------------------------------ Quantitative Trait SML Expectations ------------------------------------------------ A allele frequency = 0.050 Genotypes = A/A A/B B/B Genotype frequencies = 0.003 0.095 0.902 Genotypic means = 5.000000 0.000000 -5.000000 Genotypic SDs = 1.000000 1.000000 1.000000 Expected trait mean (SD) = -4.500000 ( 1.837117) Variances (A, D, E) = 2.375000 0.000000 1.000000 Broad heritability = 0.704 Midparent E(Child) Expected IQR ----------- ------------ ------------------------- -10.0114 -8.3784 -10.0911 -6.6656 -8.1742 -7.0856 -8.7983 -5.3728 -6.3371 -5.7928 -7.5056 -4.0800 -4.5000 -4.5000 -6.2128 -2.7872 -2.6629 -3.2072 -4.9200 -1.4944 -0.8258 -1.9144 -3.6272 -0.2017 1.0114 -0.6216 -2.3344 1.0911
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