Inference of Trait Associations with SNP Haplotypes and Other
Attributes using the EM Algorithm
K. Burkett <kburkett@uottawa.ca>, B. McNeney <mcneney@sfu.ca>, J.
Graham <jgraham@stat.sfu.ca>, with code for case-control data
contributed by Zhijian Chen <z11chen@math.uwaterloo.ca>

Estimate Haplotype Relative Risks in Case-Control Data
'haplo.ccs' estimates haplotype and covariate relative risks in case-control data by weighted logistic regression. Diplotype probabilities, which are estimated by EM computation with progressive insertion of loci, are utilized as weights.

'haplo.ccs' estimates haplotype and covariate relative
risks in case-control data by weighted logistic regression.
Diplotype probabilities, which are estimated by EM computation
with progressive insertion of loci, are utilized as weights.

Benjamin French[aut, cre],
Thomas Lumley[aut, cre],
Shawn Garbett[ctb]
Haplotype and covariate relative risks in case-control data are estimated by weighted logistic regression. Diplotype probabilities, which are estimated by EM computation with progressive insertion of loci, are utilized as weights. French et al. (2006) <doi:10.1002/gepi.20161>.

Score Tests for Association of Traits with Haplotypes when
Linkage Phase is Ambiguous.
Charles M. Rowland, David E. Tines, and Daniel J. Schaid
<schaid@mayo.edu>.  R version translation by Gregory R. Warnes
<gregory_r_warnes@groton.pfizer.com>
A suite of routines that can be used to compute score
statistics to test associations between haplotypes and a wide
variety of traits, including binary, ordinal, quantitative, and
Poisson. These methods assume that all subjects are unrelated and
that haplotypes are ambiguous (due to unknown linkage phase of the
genetic markers). The methods provide several different global and
haplotype-specific tests for association, as well as provide
adjustment for non-genetic covariates and computation of simulation
p-values (which may be needed for sparse data). Details on the
background and theory of the score statistics can be found in the
following reference:

Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA.
Score tests for association of traits with haplotypes when
linkage phase is ambiguous. American J Human Genetics, February,
2002.
Copyright 2001 Mayo Foundation for Medical Education
and Research.

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