haplo.score.glm {haplo.stats} | R Documentation |
This function is used by haplo.score when analyzing traits by a GLM score.
haplo.score.glm(y, mu, a, v, x.adj, nreps, x.post, post, x)
y |
Vector of trait values. |
mu |
Expected value of y. |
a |
scale parameter |
v |
v= b''/a for a GLM. |
x.adj |
Matrix of non-genetic covariates used to adjust the score statistics. Note that intercept should be included in this matrix. |
nreps |
Vector for the count of haplotype pairs that map to each subject's marker genotypes (see haplo.em). |
x.post |
Matrix for posterior mean of x per subject. |
post |
Vector of posterior probabilities of pairs of haplotypes for a person, given thier marker phenotypes (see haplo.em). |
x |
Matrix of scores for enumerated haplotypes for each subject, with elements 0, 1, 2 (counts of specific haplotypes). |
None.
Using posterior probabilities of pairs of haplotypes, the "design" matrix for the haplotype effects, and the GLM residuals, compute the score vector and its variance matrix, adjusted for the non-genetic covariates.
List with components:
u.score |
Vector of scores for the chosen haplotypes |
v.score |
Covariance matrix for u.score |
Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA. Score tests for association of traits with haplotypes when linkage phase is ambiguous. Submitted to Amer J Hum Genet.
haplo.score