\name{X.snp.matrix-class}
\docType{class}
\alias{X.snp.matrix-class}
\alias{initialize,X.snp.matrix-method}
\alias{[,X.snp.matrix-method}
\alias{[,X.snp.matrix,ANY,ANY,ANY-method}
\alias{[<-,X.snp.matrix,ANY,ANY,X.snp.matrix-method}
\alias{coerce,X.snp.matrix,character-method}
\alias{coerce,snp.matrix,X.snp.matrix-method}
\alias{show,X.snp.matrix-method}
\alias{summary,X.snp.matrix-method}

\title{Class "X.snp.matrix"}
\description{This class extends the  \code{\link{snp.matrix-class}} to
    deal with SNPs on the X chromosome.}
\section{Objects from the Class}{
Objects can be created by calls of the form \code{new("X.snp.matrix", x,
  Female)}.
Such objects have an additional \code{slot} to objects of class
\code{"snp.matrix"}
consisting of  a logical array of the same length as the number of
rows. This array indicates whether the sample corresponding to that row
came from a female (\code{TRUE}) or a male (\code{FALSE}). 
}
\section{Slots}{
	 \describe{
    \item{\code{.Data}:}{Object of class \code{"matrix"} and storage mode
      \code{"raw"}} 
    \item{\code{Female}:}{Object of class \code{"logical"} indicating
      sex of samples}
  }
}
\section{Extends}{
Class \code{"snp.matrix"}, directly, with explicit coerce.
Class \code{"matrix"}, by class \code{"snp.matrix"}.
Class \code{"structure"}, by class \code{"snp.matrix"}.
Class \code{"array"}, by class \code{"snp.matrix"}.
Class \code{"vector"}, by class "snp.matrix", with explicit coerce.
Class \code{"vector"}, by class "snp.matrix", with explicit coerce.
}
\section{Methods}{
  \describe{
    \item{[}{\code{signature(x = "X.snp.matrix")}: subset
      operations}
    \item{[<-}{\code{signature(x = "X.snp.matrix")}: subset
      assignment operation to replace part of an object}
    \item{coerce}{\code{signature(from = "X.snp.matrix", to =
	"character")}:  map to codes 0, 1, 2, or NA}
    \item{coerce}{\code{signature(from = "snp.matrix", to =
	"X.snp.matrix")}:
      maps a snp.matrix to an X.snp.matrix. Sex is inferred from the
      genotype data since males should not be heterozygous at any locus.
      After inferring sex, heterozygous calls for males are set to
      \code{NA}}
     \item{show}{\code{signature(object = "X.snp.matrix")}: map to codes
      "A/A", "A/B", "B/B", "A/Y", "B/Y" or ""}
    \item{summary}{\code{signature(object = "X.snp.matrix")}: returns
      the sex distribution, together with
      summaries of the data frames returned by
      \code{\link{row.summary}} and \code{\link{col.summary}}}
  }
}
\references{\url{http://sourceforge.net/projects/outmodedbonsai/}}
\author{David Clayton \email{david.clayton@cimr.cam.ac.uk}}
\seealso{\code{\link{X.snp-class}}, \code{\link{snp.matrix-class}},
    \code{\link{snp-class}}
}
\examples{
data(testdata)
summary(Xchromosome)

# display the first 10 snps of the first 10 samples
print(as(Xchromosome[1:10,1:10],'character'))

# convert the empty strings (no-calls) explicitly to "NC" before
# writing to an (anonymous and temporary) csv file
csvfile <- tempfile()
write.csv(file=csvfile, gsub ('^$', 'NC',
                              as(Xchromosome[1:10,1:10], 'character')
                             ), quote=FALSE)
unlink(csvfile)
}
\keyword{classes}