\HeaderA{genotypeSummary}{print the summary of genotypes sorted by markers}{genotypeSummary}
\keyword{misc}{genotypeSummary}
\begin{Description}\relax
print the summary of genotypes sorted by markers
\end{Description}
\begin{Usage}
\begin{verbatim}
genotypeSummary(object, 
                by = NULL, 
                confidence = 0.95, 
                alpha = 1 - confidence, 
                show = TRUE, 
                HWE.method = c("simulate", "exact"), 
                simulate.p.value = TRUE, 
                B = 10000, 
                verbose = FALSE, 
                includeOverall = FALSE, 
                omitRepeats = TRUE, 
                founderOnly = FALSE, 
                ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] geneSet object 
\item[\code{by}] optional column name, by which the summary is
desired. Default is NULL. 
\item[\code{confidence}] confidence intervals of Genotype frequencies within
each marker (default is 95\%) 
\item[\code{alpha}] Type -1 error rate = (1- confidence) 
\item[\code{show}] No longer used 
\item[\code{HWE.method}] Method to be used for Hardy-Weinberg Equilibrium
Significance Test, exact or simulate 
\item[\code{simulate.p.value}] No longer used 
\item[\code{B}] No longer used 
\item[\code{verbose}] No longer used
\item[\code{includeOverall}] logical value (TRUE/FALSE) indicating whether
overall summary is also needed, default = FALSE 
\item[\code{omitRepeats}] logical value (TRUE/FALSE) indicating whether
Gene name and marker name should be printed repeatedly for each Genotype, default = TRUE 
\item[\code{founderOnly}] logical value (TRUE/FALSE) indicating whether
founder information should be extracted from the geneSet object, default = FALSE 
\item[\code{...}] any further arguments to print
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
We can print the genotypeSummary on screen, or save in .html
format or .tex format
\end{Details}
\begin{Author}\relax
Nitin Jain \email{nitin.jain@pfizer.com}
\end{Author}
\begin{Examples}
\begin{ExampleCode}
library(GeneticsBase)
data(CAMP)

temp <- genotypeSummary(CAMP)

print(temp)
txt(temp, filename="genotypeSummary.txt")
html(temp, filename="genotypeSummary.html")
latex(temp, filename="genotypeSummary.tex")

\end{ExampleCode}
\end{Examples}

