Description Usage Arguments Details Value References
This functions actually includes two association tests which differ only at the estimation of the variance of score statistic by option 'method'. It uses regular formula for Var_{case}(E(G_{ij}|D_{ij})) when method = 'Regular' (also called likelihood method in the paper), Var_{case}(G_{ij}) is used for Var_{case}(E(G_{ij}|D_{ij})) when method = 'RVS'. It uses the population frequency P to estimate variance for case if method=RVS, otherwise use the expected genotype probability for case directly.
1 | RVS_asy(Y, X, P, RVS = "TRUE")
|
Y |
- a vector with the phenotype for n individuals (=ncase+ncont), first ncase (y=1) then ncont (y=0) (integar) |
X |
- a vector of genotype for a snp, first ncase and then ncont |
P |
(vector with length 3 (double)) - estimated genotype frequency for a variant P(G=0), P(G=1) and P(G=2) |
RVS, |
logic variable to indicate the estimation of variance of the score statistic. |
Note, both function scaled the variance in equation (1) in Appendix A by dividing N_case*Ncontrol/N also note the test statistics in anova gives us Rao=s^2/var(s^2), where RVS=s^2/robust var(s^2) so RVS=Rao *var(s^2)/robust var(s^2), s=sum(y_j-mean(y))E(G_ij|D_ij), therefore var(s)//var(E(Gij|Dij)), var(X) in code.
p-values for the snp
http://www.ncbi.nlm.nih.gov/pubmed/22570057
http://www.ncbi.nlm.nih.gov/pubmed/24733292
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