MCPerm (version 1.1.4)

OR.MCPerm: A Monte Carlo permutation method for multiple OR(odd ratio) test correction in case/control association study

Description

A Monte Carlo permutation method for multiple OR(odd ratio) test correction in case/control association study.

Usage

OR.MCPerm(case_allele1, case_allele2, control_allele1, control_allele2, repeatNum = 1000)

Arguments

case_allele1

a non-negative integer, the frequency of allele1 in case samples.

case_allele2

a non-negative integer, the frequency of allele2 in case samples.

control_allele1

a non-negative integer, the frequency of allele1 in control samples.

control_allele2

a non-negative integer, the frequency of allele2 in control samples.

repeatNum

an integer(default 1000) specifying the number of replicates used in the Monte Carlo permutation.

Value

risk_allele

risk_allele.

pValue

the p value for the test.

obsOR

the OR value for the true data.

permOR

a vector with 'repeatNum' elements, the OR value for the simulation data.

Details

The odds ratio is a measure of effect size, describing the strength of association or non-independence between two binary data values.

"OR.MCPerm" simulates permutation method to get p value for risk_allele, by generating random numbers for the hypergeometric distribution based on the genotype statistic of original data. Seealso chisq.MCPerm.

References

William S Noble(Nat Biotechnol.2009): How does multiple testing correction work?

Edwards, A.W.F.(1963): The measure of association in a 2x2 table.

Edgington. E.S.(1995): Randomization tests, 3rd ed.

See Also

OR, OR.TradPerm, Armitage, Armitage.TradPerm, Armitage.MCPerm, chisq.test, chisq.TradPerm, chisq.MCPerm, fisher.test, fisher.TradPerm, fisher.MCPerm, meta, meta.TradPerm, meta.MCPerm, permuteGenotype, rhyper, permuteGenotypeCount, genotypeStat

Examples

# case_allele1=23
# case_allele2=34
# control_allele1=26
# control_allele2=29
# OR.MCPerm(23,34,26,29,repeatNum=100000)