Armitage: Armitage's trend test for the 2x3 genotype table

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

View source: R/Armitage.R

Description

Armitage's trend test for the 2x3 genotype table.

Usage

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Armitage(case_11, case_12, case_22, control_11, control_12, control_22)

Arguments

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.

Details

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.

Value

statistic

numeric, the statistic of armitage test for trend.

pValue

numeric, the p value of armitage test for trend.

Author(s)

Lanying Zhang and Yongshuai Jiang <[email protected]>

References

Armitage, P(1955): Tests for Linear Trends in Proportions and Frequencies.

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

See Also

OR, OR.TradPerm, OR.MCPerm, 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

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# case_11=4
# case_12=1
# case_22=1
# control_11=3
# control_12=0
# control_22=0
# Armitage(case_11,case_12,case_22,control_11,control_12,control_22)

Example output

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).

MCPerm documentation built on May 29, 2017, 11:27 a.m.