Learn R Programming

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

Run this code
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)
}

Run the code above in your browser using DataLab