haplo.score.podds {haplo.stats} | R Documentation |
This function is used by haplo.score when analyzing ordinal traits by a proportional odds model score statistic.
haplo.score.podds(y, alpha, beta=NA, x.adj=NA, nreps, x.post, post, x)
y |
Vector of ordinal trait values. |
alpha |
Intercept parameters for ordinal logistic regression model. |
beta |
Regression parameters for adjusted covariates (x.adj). |
x.adj |
Matrix of non-genetic covariates used to adjust the score statistics. Note that intercept should NOT 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 proportional odds model, 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 |
To analyze an ordinal trait with adjustment for x.adj covariates, the user will need to have Frank Harrell's librarys (Design and Hmisc). However, the unadjusted ordinal trait works fine without these libraries.
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