\name{Armitage}
\alias{Armitage}
\alias{Armitage.default}
\alias{ArmitageTest}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{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)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{geneSetObj}{a geneSet object}
  \item{pedObj}{a pedigree object}
  \item{method}{genotype coding method. The default is additive coding (\code{A}). The other two available coding methods are recessive coding (\code{R}) and dominant coding (\code{D}), respectively.}
  \item{x}{ a vector of bialleleic markers coded by additive, recessive, or dominant model.
Denote B as common allele and A as minor allele.
  \item{additive model:}{x=0 -- BB; x=1 -- AB; x=2 -- AA}
  \item{recessive model:}{x=0 -- BB; x=0 -- AB; x=2 -- AA}
  \item{dominant model:}{x=0 -- BB; x=1 -- AB; x=1 -- AA}
}
  \item{mem}{disease membership. \code{1} -- case; \code{0} -- control}
}
\details{
}
\value{
  The functions \code{Armitage} and \code{Armitage.default} return a matrix with \code{nMarkers} rows and 2 columns, where \code{nMarkers} is the number of markers. The two columns are test statistic (\code{stat}) and p-value (\code{pvalue}), respectively.

  The function \code{ArmitageTest} returns a list of two elements:
  \item{stat }{test statistic}
  \item{pvalue }{p-value of the test}

}
\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.
}
\author{ 
  Gregory Warnes <warnes@bst.rochester.edu>
  Ross Lazarus <ross.lazarus@channing.harvard.edu>
  Weiliang Qiu <stwxq@channing.harvard.edu>
 }
\note{
This implementation is based on the documentation at webpage:
\url{http://linkage.rockefeller.edu/pawe3d/help/Linear-trend-test-ncp.html}.
}
\seealso{ }
\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))

}
\keyword{ misc }