\HeaderA{desMarkers}{Descriptive statistics for markers}{desMarkers}
\keyword{htest}{desMarkers}
\begin{Description}\relax
Descriptive statistics for markers.
\end{Description}
\begin{Usage}
\begin{verbatim}
desMarkers(geneSetObj,
           founderOnly=TRUE,
           thrsh=0.05,
           HWE.method=c("simulate","exact"),
           simulate.p.value=FALSE,
           B=10000,
           markerThrsh=100,
           maxDist=5,
           LDmeasure="r2",
           plot=TRUE,
           ...)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{geneSetObj}] a \code{geneSet} object.
\item[\code{founderOnly}] indicates if using only founder info
\item[\code{thrsh}] threshold for Hardy-Weinberg equilibrium test. If the pvalue of the HWE test for a marker is greater than \code{thrsh}, then the marker is a good marker.
\item[\code{HWE.method}] method to do Hardy-Weinberg equilibrium test.
\item[\code{simulate.p.value}] indicates if the pvalue of the HWE test is calculated by Monte Carlo simulation. \code{simulate.p.value=FALSE} means the pvalue is calculated from asymptotic chi-squared distribution of the test statistic. Otherwise, Monte Carlo simulation is used to calculate pvalue. For more details, please refers to the \code{R} function \code{chisq.test}.
\item[\code{B}] the number of replicates used in Monte Carlo simulation to get the pvalue of HWE test. For more details, please refers to the \code{R} function \code{chisq.test}.
\item[\code{markerThrsh}] if the number of markers is greater than this threshold, then 'LDdist' is called instead of 'LD'.
\item[\code{maxDist}] the width of window used in 'LDdist' function.
\item[\code{LDmeasure}] indicates if \code{r\textasciicircum{}2} or \code{D'} is to be plot.
\item[\code{plot}] indicates if LD plot is output or not.
\item[\code{...}] Other arguments that are used by HWE.chisq or HWE.exact.
\end{ldescription}
\end{Arguments}
\begin{Value}
a data frame contains components: 
\begin{ldescription}
\item[\code{Name}] marker names
\item[\code{Position}] marker positions
\item[\code{ObsHET}] marker's observed heterozygosity (i.e., proportion of heterozygotes at markes). Missing alleles are excluded in the calculation.
\item[\code{PredHET}] marker's predicted heterozygosity (i.e., \code{2*MAF*(1-MAF)}). Missing alleles are excluded in the calculation.
\item[\code{HWpval}] pvalues for Hardy-Weinberg test
\item[\code{pGeno}] percentage of non-missing genotypes for markes
\item[\code{MAF}] minor allele frequencies. missing allele are excluded from calculation
\item[\code{Rating}] \code{Rating[i]=1} means that the $i$-th marker passes HW test (do not reject H0 that HW equilibrium holds). \code{Rating[i]=0} means HW equilibrum does hold for the $i$-th marker.
\end{ldescription}
\end{Value}
\begin{Author}\relax
Weiliang Qiu \email{stwxq@channing.harvard.edu}, Ross Lazarus \email{ross.lazarus@channing.harvard.edu}
\end{Author}
\begin{Examples}
\begin{ExampleCode}
  #data(CAMP)
  #res<-desMarkers(CAMP)
  #print(res)
\end{ExampleCode}
\end{Examples}

