gcp: Permutation tests using GENECOUNTING

In gap: Genetic Analysis Package

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

\insertRef

zhao00gap

\insertRef

zhao04gap

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)

gap documentation built on Aug. 26, 2023, 5:07 p.m.