single.haplotype.test: single haplotype test
In HapEstXXR: Multi-Locus Stepwise Regression

Description Usage Arguments Details Value Author(s) References See Also

Association test based on haplotypes. Haplotypes are estimated by EM algorithm.

 single.haplotype.test(snps, trait, famid, patid, fid, mid, 
           adj.var = NULL, type = c("gaussian", "binomial", "families"),
           prt = TRUE, lim = 0.05, min.count = 10, 
           alpha = 0.05, sort = FALSE)

`snps`	(n.m)-Matrix; n=No. of individuals; m=no. of SNPs; Rohde-Code
`trait`	numeric; Outcome, phenotype
`famid`	vector; Identifier for every family; only need in case of type=families
`patid`	vector; Identifier for every individuals; only need in case of type=families
`fid`	vector; Identifier for father (0=unkown); only need in case of type=families
`mid`	vector; Identifier for mother (0=unkown); only need in case of type=families
`adj.var`	(n,m)-Matrix; n=No. of individuals; m=no. of covariates; variables for adjustment; in case of type=families not available.
`type`	type of depending variable
`lim`	numeric; threshold for pooling of haplotypes and declare as rare.
`min.count`	Minimal count for using pooled rare haplotypes in the analysis.
`prt`	A logical value (TRUE or FALSE). If TRUE, an overview is printed.
`alpha`	In case of type=binomial the (1-alpha/2)-confidence intervals are computed.
`sort`	A logical value (TRUE or FALSE). Only usable with family data. If TRUE, families are sorted by famid and generation which is a condition of wTDT.

Haplotypes are infered by EM algorithm (Excoffier and Slatkin 1995).

For normal distributed phenotypes from independent individuals we prefer an F test and for case control data we prefer the likelihood ratio test (logistic regression) in comparison of full model with genetic and non-genetic factors to a reduced model, which includes only non-genetic variables. In the case of no specified non-genetic variable only the intercept is used. If one of these tests are significance we assume a genetic effect. In case of family data the weigthed TDT statistic is used.