gcp {gap}

Permutation tests using GENECOUNTING

Description

Permutation tests using GENECOUNTING

Usage

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

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.

Details

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

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.

Note

Built on gcp.c.

Author(s)

Jing Hua Zhao

References

Zhao JH, Curtis D, Sham PC (2000). “Model-free analysis and permutation tests for allelic associations.” Hum Hered, 50(2), 133-9. ISSN 0001-5652 (Print) 0001-5652, doi:10.1159/000022901.

Zhao JH (2004). “2LD. GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis.” Bioinformatics, 20(8), 1325-6. ISSN 1367-4803 (Print) 1367-4803, doi:10.1093/bioinformatics/bth071.

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

See Also

genecounting

Examples

## 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")

## End(Not run)