anova_hapassoc: Return likelihood ratio test of haplotype effect

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

Return likelihood ratio test of haplotype effect

Description

This function returns the likelihood ratio test statistic comparing two nested models fit with hapassoc for cohort or cross-sectional data.

Usage

## S3 method for class 'hapassoc'
anova(object, redfit, display=TRUE, ...)

Arguments

object

a list of class hapassoc output by the hapassoc function

.

redfit	A hapassoc object resulting from fitting a reduced model
display	An indicator to suppress output displayed on screen
...	additional arguments to the summary function currently unused

Details

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

Value

LRTstat	The likelihood ratio statistic comparing the two models
df	Degrees of freedom of the likelihood ratio statistic
pvalue	The p-value of the test

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)
example2.regr <- hapassoc(affected ~ attr + hAAA+ hACA + hACC + hCAA + 
pooled, example2.pre.hapassoc, family=binomial())
example2.regr2 <- hapassoc(affected ~ attr + hAAA, example2.pre.hapassoc, 
family=binomial())
anova(example2.regr,example2.regr2)

# Returns:

#	hapassoc: likelihood ratio test

#Full model: affected ~ attr + hAAA + hACA + hACC + hCAA + pooled 
#Reduced model: affected ~ attr + hAAA 

#LR statistic = 1.5433 , df = 4 , p-value =  0.8189 

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