R: Haplotype trend regression

htr {gap} | R Documentation

## Haplotype trend regression

### Description

Haplotype trend regression (with permutation)

### Usage

    htr(y,x,n.sim=0)

### Arguments

`y` | a vector of phenotype
`x` | a haplotype table
`n.sim` | the number of permutations

### Value

The returned value is a list containing:

`f` | the F statistic for overall association
`p` | the p value for overall association
`fv` | the F statistics for individual haplotypes
`pi` | the p values for individual haplotypes

### References

Zaykin DV, Westfall PH, Young SS, Karnoub MA, Wagner MJ, Ehm MG (2002) Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals. Hum. Hered. 53:79-91

Xie R, Stram DO (2005). Asymptotic equivalence between two score tests for haplotype-specific risk in general linear models. Genet. Epidemiol. 29:186-170

### Note

adapted from emgi.cpp, a pseudorandom number seed will be added on

### Author(s)

Dimitri Zaykin, Jing Hua Zhao

### See Also

`hap.score`

### Examples

    ## Not run:
    # 26-10-03
    # this is now part of demo
    test2<-read.table("test2.dat")
    y<-test2[,1]
    x<-test2[,-1]
    y<-as.matrix(y)
    x<-as.matrix(x)
    htr.test2<-htr(y,x)
    htr.test2
    htr.test2<-htr(y,x,n.sim=10)
    htr.test2

    # 13-11-2003
    require(gap.datasets)
    data(apoeapoc)
    apoeapoc.gc<-gc.em(apoeapoc[,5:8])
    y<-apoeapoc$y
    for(i in 1:length(y)) if(y[i]==2) y[i]<-1
    htr(y,apoeapoc.gc$htrtable)

    # 20-8-2008
    # part of the example from useR!2008 tutorial by Andrea Foulkes
    # It may be used beyond the generalized linear model (GLM) framework
    HaploEM <- haplo.em(Geno,locus.label=SNPnames)
    HapMat <- HapDesign(HaploEM)
    m1 <- lm(Trait~HapMat)
    m2 <- lm(Trait~1)
    anova(m2,m1)

    ## End(Not run)

[Package gap version 1.2.2 Index]