gap: gcp – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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

`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

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.

Note

Built on gcp.c

Author(s)

Jing Hua Zhao

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

Genetic Analysis Package

v1.2.3-1

GPL (>= 2)

Authors

Jing Hua Zhao and colleagues with inputs from Kurt Hornik and Brian Ripley

Initial release

2021-4-21

gcp