Armitage {GeneticsBase}R Documentation

Cochran-Armitage test for linear trends in proportions and frequencies

Description

Cochran-Armitage test for linear trends in proportions and frequencies.

Usage

Armitage(geneSetObj, method="A")
Armitage.default(pedObj, method="A")
ArmitageTest(x, mem)

Arguments

geneSetObj a geneSet object
pedObj a pedigree object
method genotype coding method. The default is additive coding (A). The other two available coding methods are recessive coding (R) and dominant coding (D), respectively.
x a vector of bialleleic markers coded by additive, recessive, or dominant model. Denote B as common allele and A as minor allele.
additive model:
x=0 – BB; x=1 – AB; x=2 – AA
recessive model:
x=0 – BB; x=0 – AB; x=2 – AA
dominant model:
x=0 – BB; x=1 – AB; x=1 – AA
mem disease membership. 1 – case; 0 – control

Details

Value

The functions Armitage and Armitage.default return a matrix with nMarkers rows and 2 columns, where nMarkers is the number of markers. The two columns are test statistic (stat) and p-value (pvalue), respectively.
The function ArmitageTest returns a list of two elements:

stat test statistic
pvalue p-value of the test

Note

This implementation is based on the documentation at webpage: http://linkage.rockefeller.edu/pawe3d/help/Linear-trend-test-ncp.html.

Author(s)

Gregory Warnes <warnes@bst.rochester.edu> Ross Lazarus <ross.lazarus@channing.harvard.edu> Weiliang Qiu <stwxq@channing.harvard.edu>

References

Gordon D, Haynes C, Blumenfeld J, Finch SJ (2005) PAWE-3D: visualizing Power for Association With Error in case/control genetic studies of complex traits. Bioinformatics 21:3935-3937.

Gordon D, Finch SJ, Nothnagel M, Ott J (2002) Power and sample size calculations for case-control genetic association tests when errors are present: application to single nucleotide polymorphisms. Hum Hered 54:22-33.

Chapman, D.G. and Nam, J.M. (1968) Asymptotic power of chi square tests for linear trends in proportions. Biometrics. 24, 315-327.

Armitage, P. (1955) Tests for linear trends in proportions and frequencies. Biometrics. 11, 375-386.

Cochran, W.G. (1954) Some methods for strengthening the common chi-squared tests. Biometrics. 10, 417-451.

See Also

Examples

  # not significant result
  ArmitageTest(x=c(2,1,1,1,0,0,1,0,0,1), mem=c(1,1,1,1,1,0,0,0,0,0))

  # significant result
  ArmitageTest(x=c(2,2,1,1,0,0,0,0,0,0), mem=c(1,1,1,1,1,0,0,0,0,0))


[Package GeneticsBase version 1.2.0 Index]