Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm
Return likelihood ratio test of haplotype effect
EM algorithm to fit maximum likelihood estimates of trait associations...
Simulated data for a hypothetical binary trait
Simulated data for a hypothetical genetic SNPs
Return log-likelihood
Pre-process the data before fitting it with hapassoc
Summarize results of the hapassoc function
The following R functions are used for inference of trait associations with haplotypes and other covariates in generalized linear models. The functions are developed primarily for data collected in cohort or cross-sectional studies. They can accommodate uncertain haplotype phase and handle missing genotypes at some SNPs.