\HeaderA{html}{Generate summary table files for genotype objects}{html}
\methaliasA{html.GeneticsBaseSummary}{html}{html.GeneticsBaseSummary}
\methaliasA{html.LD}{html}{html.LD}
\methaliasA{html.markerSummary}{html}{html.markerSummary}
\aliasA{latex}{html}{latex}
\methaliasA{latex.default}{html}{latex.default}
\methaliasA{latex.GeneticsBaseSummary}{html}{latex.GeneticsBaseSummary}
\methaliasA{latex.LD}{html}{latex.LD}
\methaliasA{latex.markerSummary}{html}{latex.markerSummary}
\aliasA{print.GeneticsBaseSummary}{html}{print.GeneticsBaseSummary}
\aliasA{txt}{html}{txt}
\methaliasA{txt.default}{html}{txt.default}
\methaliasA{txt.GeneticsBaseSummary}{html}{txt.GeneticsBaseSummary}
\methaliasA{txt.LD}{html}{txt.LD}
\methaliasA{txt.markerSummary}{html}{txt.markerSummary}
\keyword{misc}{html}
\begin{Description}\relax
Generate summary table files for genotype objects
\end{Description}
\begin{Usage}
\begin{verbatim}
#### HTML file format
html
## S3 method for class 'LD':
html(x, filename = "", digits = 3, ...)
## S3 method for class 'GeneticsBaseSummary':
html(x, filename = "", ...)
## S3 method for class 'markerSummary':
html(x, filename = "", plot.format = "pdf", 
                   sep=".", verbose=TRUE, ...)

#### plain text file format
txt
## Default S3 method:
txt(x, filename="", eol="\n", ...)
## S3 method for class 'markerSummary':
txt(x, filename = "", plot.format = "pdf",
                   sep=".", verbose=TRUE, ...)

#### LaTex file format
latex
## Default S3 method:
latex(x, filename="", ...)
## S3 method for class 'LD':
latex(x, filename = "", digits = 3, ...)
## S3 method for class 'GeneticsBaseSummary':
latex(x, filename = "", ...)
## S3 method for class 'markerSummary':
latex(x, filename = "", plot.format = "pdf",
                   sep=".", verbose=TRUE, ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] Object to be rendered to html/txt/latex
\item[\code{filename}] Output filename, see below for details.
\item[\code{eol}] End of line marker, defaults to \code{"\bsl{}n"}. MS-DOS/MS-Windows
uses \code{"\bsl{}r\bsl{}n"} 
\item[\code{digits}] Number of digits to display
\item[\code{plot.format}] Graphics format for LD plot. Only \code{"pdf"} is
currently supported
\item[\code{sep}] Separatior used to join the file prefix provided by
\code{filename} and descriptive text when generating file names
\item[\code{verbose}] Show names of created files.
\item[\code{...}] Additional parameters to pass to component methods
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
For \code{alleleSummary}, \code{genotypeSummary}, and \code{LD}
objects, the \code{filename} argument is either the exact name of the file to
be created, or "" which will print the output to the console.

For \code{markerSummary} objects, \code{filename} may be either
\code{""} or a prefix used to create file names. If \code{filename=""}
all output is printed to the R console.  Otherwise, filenames for each
component are constructed by combining the prefix specified by
\code{filename}, the separator specified by \code{sep}, a string
descibing the file contents (one of "alleleSummary",
"genotypeSummary", and "LD"), and the file extension ".html".
\end{Details}
\begin{Value}
Nothing of interest
\end{Value}
\begin{Author}\relax
Nitin Jain \email{nitin\_jain@pfizer.com} and
Gregory R. Warnes \email{warnes@bst.rochester.edu}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{alleleSummary}{alleleSummary}},
\code{\LinkA{genotypeSummary}{genotypeSummary}},
\code{\LinkA{markerSummary}{markerSummary}},
\code{\LinkA{LD}{LD}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
data(CAMP)

###
# Generate a plain text allele summary table
###
aS <- alleleSummary(CAMP)
# display inline
txt(aS, filename="")
# create CAMP_alleleSummary.txt
txt(aS, filename="CAMP.alleleSummary.html") 

###
# Generate an HTML genotype summary table
###
gS <- genotypeSummary(CAMP)
# display inline
html(gS, filename="")
# create CAMP_genotypeSummary.html
html(gS, filename="CAMP.genotypeSummary.html")

###
# Generate a LaTeX Linkage Disequilibrium table
###
ld <- LD(CAMP)
# display inline
latex(ld, filename="")
# create CAMP_LDSummary.html
latex(ld, filename="CAMP.LD.html")

###
# Generate a complete set of summary tables 
###
mS <- markerSummary(CAMP)
# Plain text format
txt(mS, filename="CAMP", sep="_")
# HTML format
html(mS, filename="CAMP", sep="_")
# LaTeX format
latex(mS, filename="CAMP", sep="_")

\end{ExampleCode}
\end{Examples}

