gee.sibs.or | R Documentation |
Use GEE to estimate a common sib-sib odds ratio for a binary phenotype, adjusting for covariates with a logistic model.
gee.sibs.or(y, x, id, beta = NULL, gamma = 0.5, give.se = TRUE,
return.intercept = FALSE, maxit = 1000, tol = 0.00001,
eta.tol = 0.000000001, trace = FALSE, debug = FALSE,
method = c("gee2", "gee1", "identity"))
y |
A vector of binary phenotypes (coded 0/1). |
x |
A numeric matrix of covariates, including an intercept term. |
id |
A vector of integers indicating family/group assignment. |
beta |
Optional starting values for the covariate coefficients; if
|
gamma |
Optional starting value for the log odds ratio. If
|
give.se |
If true, calculate estimated standard errors. |
return.intercept |
If TRUE, the estimate for the intercept coefficient is included in the output. |
maxit |
Maximum number of iterations. If 0, some debugging information is returned. |
tol |
Tolerance value for determining convergence in Newton's method to solve the GEE. |
eta.tol |
Tolerance value for determining convergence in Newton's method to calculate the eta parameters. |
trace |
Indicates whether to display tracing information; large indicators result in more verbose output. |
debug |
Indicates whether to display special debugging-related information. |
method |
Indicates whether to use GEE2, GEE1, or the identity matrix as the working covariance matrix. |
We assume a set of randomly ascertained sibships with measurements on a binary phenotype and a set of covariates. We use a logistic model to contact the expected phenotype and the covariates and assume a constant log odds ratio for sibs' phenotypes. Parameters are estimated using generalized estimating equations (GEE).
The idea is described in Liange and Beaty (1991). All of the details appear in Liang et al. (1992) and Qaqish (1990).
Key bits are coded in C; but there's still a lot done directly in R. Eventually I'd like to move more of the code to C, for the sake of speed.
If give.se=TRUE
, the output is a matrix with four columns:
the parameter estimates, estimated SEs, (est/SE)^2
, and P-values. If
give.se=FALSE
, a vector with only the parameter estimates is given.
The first item is the sib-sib log odds ratio; the rest are the covariates'
coefficients; if return.intercept=FALSE
, the intercept is excluded
from the output.
Karl W Broman, broman@wisc.edu
Liang, K.-Y. and Beaty, T. H. (1991) Measuring familial aggregation by using odds-ratio regression models. Genetic Epidemiology, 8, 361–370.
Liang, K.-Y., Zeger, S. L. and Qaqish, B. (1992) Multivariate regression analyses for categorical data (with discussion). J. Roy. Statist. Soc. B, 1, 3–40.
Qaqish, B. F. (1990) Multivariate regression models using generalized estimating equations. Ph. D. Thesis, Department of Biostatistics, Johns Hopkins University, Baltimore, Maryland.
fake.data()
data(fake.data)
y <- fake.data[,1]
id <- fake.data[,2]
x <- cbind(1, fake.data[,-(1:2)])
gee.output <- gee.sibs.or(y, x, id, trace=TRUE)
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