Recently I'm working with functional candidate gene study. so I have three SNP and need to calculate allele substitution effect and additive and dominance effect for single SNP marker association with quantitative traits (i.e body weight). can anyone give me best statistical way to do this.
The easiest way would be through a linear regression (you can use R, SAS, even MS Excel). All what you have to do is to code your alleles as 0-1-2 {AA, Aa, aa}, then regress the phenotype over that SNP. Simple like that: The beta coefficient is you effect of an allele substitution.
For dominance, the procedure is the same, but you code you alleles as 0-1-0 {AA, Aa, aa}. You may want to consider fit both additive and dominance effect at the same time. In which case, the regression coefficient of dominance indicate what kind of dominance this locus display (under dominance, over dominance, complete dominance, etc.).
The easiest way would be through a linear regression (you can use R, SAS, even MS Excel). All what you have to do is to code your alleles as 0-1-2 {AA, Aa, aa}, then regress the phenotype over that SNP. Simple like that: The beta coefficient is you effect of an allele substitution.
For dominance, the procedure is the same, but you code you alleles as 0-1-0 {AA, Aa, aa}. You may want to consider fit both additive and dominance effect at the same time. In which case, the regression coefficient of dominance indicate what kind of dominance this locus display (under dominance, over dominance, complete dominance, etc.).
Hi Man.
The PLINK seems like the best way!
Can you use the command:
plink --file mydata --model
(The genotypic test provides a general test of association in the 2-by-3 table of disease-by-genotype. The dominant and recessive models are tests for the minor allele (which is the minor allele can be found in the output of either the --assoc or the --freq commands. That is, if D is the minor allele (and d is the major allele): Allelic: D versus d
Dominant: (DD, Dd) versus dd
Recessive: DD versus (Dd, dd)
Genotypic: DD versus Dd versus dd)
As mentioned above, these tests are generated a file plink.model
which contains the following fields:
CHR Chromosome number
SNP SNP identifier
TEST Type of test
AFF Genotypes/alleles in cases
UNAFF Genotypes/alleles in controls
CHISQ Chi-squated statistic
DF Degrees of freedom for test
P Asymptotic p-value
@Jingwei Yuan
How we can analyse on R and what type of R coding used?
@Muhammad Kashif Naeem
The 'GenABEL' Package in r can do genome-wide or single SNP association analysis.
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