Dear
Khandker
There may be various ways. One of those is to use both additive and dominance relationship coefficients.
additive relationship coefficients for SNP - 0 for absent of a particular allele, 1 for heterozygous, 2 for homozygous for the allele
dominance relationship coefficients for SNP - 0 for any homozygous, 1 for heterozygous
Fitting both coefficients together in a model, you would get additive and dominance effects.
Also, following paper would be useful if you are interested in alternatives (e.g. IBD coefficients for additive and dominance effects)
Using dominance relationship coefficients based on linkage disequilibrium and linkage with a general complex pedigree to increase mapping resolution
Genetics, 174: 1009-1016
Cheers
Hong
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제목 : How to get additve and dominance effect value?
날짜 : 2008년 8월 13일 수요일, 오후 17시 31분 05초 +0900
보낸이 : Khandker Kislam <kkislam@UALBERTA.CA>
받는이 : ASREML-L@DPI.NSW.GOV.AU
Hi Discussion Group Members,
I was trying to analyze my data using ASReml, to find out association
of single nucleotide polymorphism (SNP) with phenotypic trait (in
animal data). For three different genotypes (0,1,2 in data set) of a
single SNP, I can get predicted trait values for individual genotype
and also can get allele substitution effect for a SNP. However, I am
unable to calculate the additive and dominance effect of a single SNP.
How can I get those values? [I use animal model and univariate analysis]
I appreciate suggestions and comments from you.
Best regards,
Khandker
Graduate Student
University of Alberta
Canada
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