logLik_hapassoc: Return log-likelihood

In hapassoc: Inference of Trait Associations with SNP Haplotypes and Other Attributes using the EM Algorithm

Return log-likelihood

Description

This function is used to return the log-likelihood at the maximum likelihood estimates computed by hapassoc and to return the number of parameters fit by hapassoc (i.e. the degrees of freedom in R) for cohort or cross-sectional data.

Usage

## S3 method for class 'hapassoc'
logLik(object, ...)

Arguments

object	a list of class hapassoc output by the hapassoc function
...	additional arguments to the summary function (currently unused)

Details

See the hapassoc vignette, of the same name as the package, for details.

Value

logLik	log-likelihood computed at the maximum likelihood estimates if design="cohort", or NA if design="cc"
df	number of parameters in the model (i.e. regression coefficients, any dispersion parameters and haplotype frequencies). This is not the residual degrees of freedom, which is the number of subjects minus the number of parameters estimated.

References

Burkett K, McNeney B, Graham J (2004). A note on inference of trait associations with SNP haplotypes and other attributes in generalized linear models. Human Heredity, 57:200-206

Burkett K, Graham J and McNeney B (2006). hapassoc: Software for Likelihood Inference of Trait Associations with SNP Haplotypes and Other Attributes. Journal of Statistical Software, 16(2):1-19

See Also

pre.hapassoc,hapassoc, summary.hapassoc.

Examples

data(hypoDatGeno)
example2.pre.hapassoc<-pre.hapassoc(hypoDatGeno, numSNPs=3, allelic=FALSE)
example.regr <- hapassoc(affected ~ attr + hAAA+ hACA + hACC + hCAA + 
pooled, example2.pre.hapassoc, family=binomial())
logLik(example.regr)

# Returns:
# Log Lik: -322.1558 (df=14)

hapassoc documentation built on May 28, 2022, 1:13 a.m.