gap (version 1.6)

htr: Haplotype trend regression

Description

Haplotype trend regression

Usage

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

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.

Arguments

y

a vector of phenotype.

x

a haplotype table.

n.sim

the number of permutations.

Author

Dimitri Zaykin, Jing Hua Zhao

Details

Haplotype trend regression (with permutation)

References

zaykin02gap

xie05gap

See Also

hap.score

Examples

if (FALSE) {
# 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)
}