Armitage.MCPerm: A Monte Carlo permutation method for Armitage's trend test in...
In MCPerm: A Monte Carlo permutation method for multiple test correlation

Description Usage Arguments Details Value Author(s) References See Also Examples

A Monte Carlo permutation method for Armitage's trend test in case/control association study.

1 2	Armitage.MCPerm(case_11, case_12, case_22, control_11, control_12, control_22, repeatNum = 1000)

`case_11`	a non-negative integer, the frequency of genotype "allele1/allele1" in case samples.
`case_12`	a non-negative integer, the frequency of genotype "allele1/allele2" in case samples.
`case_22`	a non-negative integer, the frequency of genotype "allele2/allele2" in case samples.
`control_11`	a non-negative integer, the frequency of genotype "allele1/allele1" in control samples.
`control_12`	a non-negative integer, the frequency of genotype "allele1/allele2" in control samples.
`control_22`	a non-negative integer, the frequency of genotype "allele2/allele2" in control samples
`repeatNum`	an integer(default 1000) specifying the number of replicates used in the Monte Carlo permutation.

The Cochran-Armitage test for trend, is used in categorical data analysis when the aim is to assess for the presence of an association between a variable with two categories and a variable with k categories. It modifies the Pearson chi-squared test to incorporate a suspected ordering in the effects of the k categories of the second variable. The trend test is ofen used as a genotype-based test for case/control genetic association studies.

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

`pValue`	the p value for the test.
`obsStatistic`	the statistic of Armitage's trend test for the true data.
`obsP`	the p value for Armitage's trend test of the true data.
`permStatistic`	a vector with 'repeatNum' elements, the statistic of Armitage's trend test for the simulation data.
`permP`	a vector with 'repeatNum' elements, the p value for Armitage's trend test for the simulation data.

Lanying Zhang and Yongshuai Jiang <jiangyongshuai@gmail.com>

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

statgen.org(2007): A derivation for Armitage's trend test for the 2x3 genotype table.

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

1 2	## Armitage.MCPerm(case_11=4,case_12=1,case_22=1,control_11=3, # control_12=5,control_22=7,repeatNum=10000)

Loading required package: metafor
Loading required package: Matrix
Loading 'metafor' package (version 2.0-0). For an overview 
and introduction to the package please type: help(metafor).