Chi-square and Fisher's exact test for association of loci and alleles with a factor

Chi-square and Fisher's exact test for association of loci and alleles with a factor

eco.association(eco, assoc = c("within", "between"), x,
  method = c("fisher.test", "chisq.test"), nrep = 99, adjust = "none",
  ndig = NA)

Arguments

eco	Object of class "ecogen".
assoc	"between" if the association test should be performed between a factor and a loci, or "within" if the association test should be performed between a factor and alleles within loci. For haploid data, use option "within".
x	The name of the S slot column with the groups for the association test.
method	Test method ("chisq.test" or "fisher.test"). Default is "fisher.test".
nrep	Number of repetitions for the permutation test.
adjust	Correction method of P-values for multiple tests, passed to p.adjust. Default is "none" (no correction).
ndig	Number of digits coding each alleles (e.g. 2: xx, or 3: xxx) when assoc is "within".

See also

chisq.test fisher.test fisher.test

Examples

# NOT RUN {
data(eco.test)
eco.association(eco, "within", "pop")
eco.association(eco, "within", "pop", adjust="fdr")
eco.association(eco, "within", "pop", method = "chisq.test")
eco.association(eco, "between", "pop", ndig = 1)
eco.association(eco, "between", "pop", method = "chisq.test", ndig = 1)

# }