anova.hapassoc {hapassoc} | R Documentation |
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 |
.
redfit |
A |
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