gcp: Permutation tests using GENECOUNTING

Description

This function is a R port of the GENECOUNTING/PERMUTE program which generates EHPLUS-type statistics including z-tests for individual haplotypes

Usage

gcp(y, cc, g, handle.miss=1, miss.val=0, n.sim=0,
       locus.label=NULL, quietly=FALSE)

Arguments

A column of 0/1 indicating cases and controls

analysis indicator, 0 = marker-marker, 1 = case-control

the multilocus genotype data

handle.miss

a flag with value 1 indicating missing data are allowed

miss.val

missing value

n.sim

the number of permutations

locus.label

label of each locus

quietly

a flag if TRUE will suppress the screen output

Value

The returned value is a list containing (p.sim and ph when n.sim > 0):

x2obs

the observed chi-squared statistic

pobs

the associated p value

zobs

the observed z value for individual haplotypes

p.sim

simulated p value for the global chi-squared statistic

simulated p values for individual haplotypes

References

Zhao JH, Curtis D, Sham PC (2000). Model-free analysis and permutation tests for allelic associations. Human Heredity 50(2): 133-139

Zhao JH (2004). 2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis. Bioinformatics 20: 1325-1326

Zhao JH, Qian WD Association analysis of unrelated individuals using polymorphic genetic markers -- methods, implementation and application, Royal Statistical Society 2003, Hassallt-Diepenbeek, Belgium.

Examples

Run this code

# NOT RUN {
data(fsnps)
y<-fsnps$y
cc<-1
g<-fsnps[,3:10]

gcp(y,cc,g,miss.val="Z",n.sim=5)
hap.score(y,g,method="hap",miss.val="Z")
# }