hapassoc (version 0.2)

EM: EM algorithm to fit maximum likelihood estimates of trait associations with SNP haplotypes

Description

This function takes a dataset of haplotypes in which rows for individuals of uncertain phase have been augmented by "pseudo-individuals" who carry the possible multilocus genotypes consistent with the single-locus phenotypes. The EM algorithm is used to find MLE's for trait associations with covariates in generalized linear models.

Usage

EM(form,haplos.list,baseline = "missing" ,family = binomial(),
gamma = FALSE, maxit = 50, tol = 0.001, ...)

Arguments

form

model equation in usual R format

haplos.list

list of haplotype data from PreEM

baseline

optional, haplotype to be used for baseline coding. Default is the most frequent haplotype.

family

binomial, poisson, gaussian or gamma are supported, default=binomial

gamma

initial estimates of haplotype frequencies, default values are calculated in PreEM using standard haplotype-counting (i.e. EM algorithm without adjustment for non-haplotype covariates)

maxit

maximum iterations of the EM loop, default=50

tol

convergence tolerance in terms of the maximum difference in parameter estimates between interations; default=0.001

...

additional arguments to be passed to the glm function such as starting values for parameter estimates in the risk model

Value

• it
  number of iterations of the EM algorithm
• beta
  estimated regression coefficients
• gamma
  estimated haplotype frequencies
• fits
  fitted values of the trait
• wts
  final weights calculated in last iteration of the EM loop. These are estimates of the conditional probabilities of each multilocus genotype given the observed single-locus genotypes.
• var
  joint variance-covariance matrix of the estimated regression coefficients and the estimated haplotype frequencies
• dispersionML
  maximum likelihood estimate of dispersion parameter (to get the moment estimate, use summary.EM)
• family
  family of the generalized linear model (e.g. binomial, gaussian, etc.)
• response
  trait value
• converged
  TRUE/FALSE indicator of convergence. If the algorithm fails to converge, only the converged indicator is returned.

See Also

PreEM,summary.EM,glm,family.

Examples

data(hypoDat)
example.preEM<-PreEM(hypoDat, 3)

names(example.preEM$haploDM)
# "h000"   "h001"   "h010"   "h011"   "h100"   "pooled"

# Logistic regression, baseline group: '001/001'

example.regr <- EM(affected ~ attr + h000+ h010 + h011 + h100 + pooled,
                     example.preEM, family=binomial())