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.

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.

Details

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

Note

Built on gcp.c.

References

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

Zhao JH (2004). “2LD. GENECOUNTING and HAP: computer programs for linkage disequilibrium analysis.” Bioinformatics, 20(8), 1325-6. 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.

Author

Jing Hua Zhao

Examples

if (FALSE) { # \dontrun{
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")
} # }