gap (version 1.5-1)

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
)

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

ph

simulated p values for individual haplotypes

Arguments

y

A column of 0/1 indicating cases and controls.

cc

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

g

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.

Author

Jing Hua Zhao

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.

See Also

genecounting

Examples

if (FALSE) {
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")
}