\HeaderA{homozygote}{Flag observations with specific allele patterns}{homozygote}
\aliasA{carrier}{homozygote}{carrier}
\methaliasA{carrier.geneSet}{homozygote}{carrier.geneSet}
\aliasA{dominant}{homozygote}{dominant}
\methaliasA{dominant.geneSet}{homozygote}{dominant.geneSet}
\aliasA{heterozygote}{homozygote}{heterozygote}
\methaliasA{heterozygote.geneSet}{homozygote}{heterozygote.geneSet}
\methaliasA{homozygote.geneSet}{homozygote}{homozygote.geneSet}
\aliasA{recessive}{homozygote}{recessive}
\methaliasA{recessive.geneSet}{homozygote}{recessive.geneSet}
\keyword{misc}{homozygote}
\begin{Description}\relax
\item[homozygote] Flag observatsions with identical alleles
\item[heterozygote] Flag observations with discordant alleles
\item[carrier] Flag observations containing a specified allele
\item[dominant] Flag observations containing one or more of the 
specified alleles.
\item[recessive] Flag observations containing only the 
specified alleles.
\end{Description}
\begin{Usage}
\begin{verbatim}
homozygote(object, ...)
homozygote.geneSet(object, allele.names, marker, ...)

heterozygote(object, ...)
heterozygote.geneSet(object, allele.names, marker, ...)

carrier(object, ...)
carrier.geneSet(object, allele.names, marker, ...)

dominant(object, ...)
dominant.geneSet(object, allele.names, marker, ...)

recessive(object, ...)
recessive.geneSet(object, allele.names, marker, ...)

\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{object}] \code{geneSet} object 
\item[\code{allele.names}] (optional) allele names.
\item[\code{marker}] (optional) marker names 
\item[\code{...}] (optional) additional arguments supplied
\end{ldescription}
\end{Arguments}
\begin{Value}
matrix of logicals.
\end{Value}
\begin{Author}\relax
Gregory R. Warnes \email{warnes@bst.rochester.edu}
and Nitin Jain \email{nitin.jain@pfizer.com}
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{geneSet}{geneSet}},
\code{\LinkA{extractAlleles}{extractAlleles}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}

data(CAMP)
lCAMP <- CAMP[,1:10] # 10 observations

# see the genotypes
genotypes(lCAMP)

# which ones are homozygotes?
homozygote(lCAMP)

# which ones are carriers  for allele "2"?
carrier(lCAMP, allele.names="2")

# which markers are heterozygotes for marker m709
heterozygote(lCAMP, marker="m709")

# if '1' is dominant, which ones will show the
# '1' phenotype for marker m47?
dominant(lCAMP, allele.names="1", marker="m47")

# if '2' is recessive, which ones will show the
# '2' phenotype for marker m523?
recessive(lCAMP, allele.names="2", marker="p523")

\end{ExampleCode}
\end{Examples}

