| gcp {gap} | R Documentation |
This function is a R port of the GENECOUNTING/PERMUTE program which generates EHPLUS-type statistics including z-tests for individual haplotypes
gcp( y, cc, g, handle.miss = 1, miss.val = 0, n.sim = 0, locus.label = NULL, quietly = FALSE )
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. |
The returned value is a list containing (p.sim and ph when n.sim > 0):
the observed chi-squared statistic
the associated p value
the observed z value for individual haplotypes
simulated p value for the global chi-squared statistic
simulated p values for individual haplotypes
Built on gcp.c.
Jing Hua Zhao
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.
## 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)