\HeaderA{geneSet-class}{Class "geneSet", a class for genetics data}{geneSet.Rdash.class}
\aliasA{alleleCount,geneSet-method}{geneSet-class}{alleleCount,geneSet.Rdash.method}
\aliasA{alleleLevels,geneSet-method}{geneSet-class}{alleleLevels,geneSet.Rdash.method}
\aliasA{alleles,geneSet-method}{geneSet-class}{alleles,geneSet.Rdash.method}
\aliasA{callCodes,geneSet-method}{geneSet-class}{callCodes,geneSet.Rdash.method}
\aliasA{callCodes<-,geneSet-method}{geneSet-class}{callCodes<.Rdash.,geneSet.Rdash.method}
\aliasA{carrier,geneSet-method}{geneSet-class}{carrier,geneSet.Rdash.method}
\aliasA{description,geneSet-method}{geneSet-class}{description,geneSet.Rdash.method}
\aliasA{description<-,geneSet-method}{geneSet-class}{description<.Rdash.,geneSet.Rdash.method}
\aliasA{dominant,geneSet-method}{geneSet-class}{dominant,geneSet.Rdash.method}
\aliasA{errorMetrics,geneSet-method}{geneSet-class}{errorMetrics,geneSet.Rdash.method}
\aliasA{errorMetrics<-,geneSet-method}{geneSet-class}{errorMetrics<.Rdash.,geneSet.Rdash.method}
\aliasA{geneSet}{geneSet-class}{geneSet}
\aliasA{genotypeLevels,geneSet-method}{geneSet-class}{genotypeLevels,geneSet.Rdash.method}
\aliasA{genotypes,geneSet-method}{geneSet-class}{genotypes,geneSet.Rdash.method}
\aliasA{head,geneSet-method}{geneSet-class}{head,geneSet.Rdash.method}
\aliasA{heterozygote,geneSet-method}{geneSet-class}{heterozygote,geneSet.Rdash.method}
\aliasA{homozygote,geneSet-method}{geneSet-class}{homozygote,geneSet.Rdash.method}
\aliasA{HWE,geneSet-method}{geneSet-class}{HWE,geneSet.Rdash.method}
\aliasA{LD,geneSet-method}{geneSet-class}{LD,geneSet.Rdash.method}
\aliasA{LDband,geneSet-method}{geneSet-class}{LDband,geneSet.Rdash.method}
\aliasA{LDdist,geneSet-method}{geneSet-class}{LDdist,geneSet.Rdash.method}
\aliasA{markerInfo,geneSet-method}{geneSet-class}{markerInfo,geneSet.Rdash.method}
\aliasA{markerInfo<-,geneSet-method}{geneSet-class}{markerInfo<.Rdash.,geneSet.Rdash.method}
\aliasA{markerNames,geneSet-method}{geneSet-class}{markerNames,geneSet.Rdash.method}
\aliasA{missingCodes,geneSet-method}{geneSet-class}{missingCodes,geneSet.Rdash.method}
\aliasA{missingCodes<-,geneSet-method}{geneSet-class}{missingCodes<.Rdash.,geneSet.Rdash.method}
\aliasA{nallele,geneSet-method}{geneSet-class}{nallele,geneSet.Rdash.method}
\aliasA{nmarker,geneSet-method}{geneSet-class}{nmarker,geneSet.Rdash.method}
\aliasA{nobs,geneSet-method}{geneSet-class}{nobs,geneSet.Rdash.method}
\aliasA{notes,geneSet-method}{geneSet-class}{notes,geneSet.Rdash.method}
\aliasA{notes<-,geneSet-method}{geneSet-class}{notes<.Rdash.,geneSet.Rdash.method}
\aliasA{phase,geneSet-method}{geneSet-class}{phase,geneSet.Rdash.method}
\aliasA{phase<-,geneSet-method}{geneSet-class}{phase<.Rdash.,geneSet.Rdash.method}
\aliasA{ploidy,geneSet-method}{geneSet-class}{ploidy,geneSet.Rdash.method}
\aliasA{ploidy<-,geneSet-method}{geneSet-class}{ploidy<.Rdash.,geneSet.Rdash.method}
\aliasA{recessive,geneSet-method}{geneSet-class}{recessive,geneSet.Rdash.method}
\aliasA{sampleInfo,geneSet-method}{geneSet-class}{sampleInfo,geneSet.Rdash.method}
\aliasA{sampleInfo<-,geneSet-method}{geneSet-class}{sampleInfo<.Rdash.,geneSet.Rdash.method}
\aliasA{show,geneSet-method}{geneSet-class}{show,geneSet.Rdash.method}
\aliasA{studyInfo,geneSet-method}{geneSet-class}{studyInfo,geneSet.Rdash.method}
\aliasA{studyInfo<-,geneSet-method}{geneSet-class}{studyInfo<.Rdash.,geneSet.Rdash.method}
\aliasA{tail,geneSet-method}{geneSet-class}{tail,geneSet.Rdash.method}
\aliasA{transTables,geneSet-method}{geneSet-class}{transTables,geneSet.Rdash.method}
\aliasA{transTables<-,geneSet-method}{geneSet-class}{transTables<.Rdash.,geneSet.Rdash.method}
\aliasA{[,geneSet-method}{geneSet-class}{[,geneSet.Rdash.method}
\aliasA{[[,geneSet-method}{geneSet-class}{[[,geneSet.Rdash.method}
\keyword{classes}{geneSet-class}
\begin{Description}\relax
A fundamental data structure for genetic data
\end{Description}
\begin{Section}{Objects from the Class}
Objects can be created by calls of the form \code{new("geneSet", ...)}.
~~ describe objects here ~~
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{callCodes}:] matrix of positive integers, 
giving genotype calls.  Each row is a locus (marker); 
each column is an individual (sample).  Each element 
is a row index into a matrix in the list of translation 
tables stored in the transTables slot.  Must have row 
and column names.

\item[\code{errorMetrics}:] numeric matrix, parallel to the 
callCodes matrix.  Each element gives an uncertainty measure 
for the corresponding element of the callCodes matrix.  Must 
have row and column names.

\item[\code{transTables}:] list of code translation tables.  The 
list must have names.  Each component is a matrix, and must 
include a column named "levels".

\item[\code{missingCodes}:] list of allele missing-value codes, 
parallel to the transTables list.  The list must have the same 
names as the list in the transTables slot.  Each component is 
a character vector.  Any allele symbol in component "abc" of 
the transTables list that appears in component "abc" of the 
missingCodes list is to be interpreted as a missing value by 
functions operating on the geneSet object. An empty list will be 
interpreted to mean that the data contains no missing values.

\item[\code{sampleInfo}:] Object of class \code{"data.frame"} 
\item[\code{markerInfo}:] a dataframe, with one row for each row 
in the callCodes matrix.  Must include columns "Name" and 
"TransTable".  

\item[\code{studyInfo}:] Object of class \code{"list"} ~~ 
\item[\code{description}:] Object of class \code{"character"} ~~ 
\item[\code{notes}:] Object of class \code{"character"} ~~ 
\item[\code{ploidy}:] Object of class \code{"numeric"} ~~ 
\item[\code{phase}:] 1. Yes/No for all (logical scalar)
2. Yes/No for each Marker (logical vector)
3. phaseObject (TBD): observation by marker by phase
probabilities + definitions of contigs + probability of
contigs 

}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[HWE] \code{signature(object = "geneSet")}: Hardy-Weinberg Equilibrium Significance Test 
\item[LD] \code{signature(object = "geneSet")}: ... 
\item[LDband] \code{signature(object = "geneSet")}: ... 
\item[LDdist] \code{signature(object = "geneSet")}: ... 
\item[[] \code{signature(x = "geneSet")}: ... 
\item[[[] \code{signature(x = "geneSet")}: ... 
\item[alleleCount] \code{signature(object = "geneSet")}: ... 
\item[alleleLevels] \code{signature(object = "geneSet")}: ... 
\item[alleles] \code{signature(object = "geneSet")}: ... 
\item[callCodes] \code{signature(object = "geneSet")}: ... 
\item[callCodes<-] \code{signature(object = "geneSet")}: ... 
\item[carrier] \code{signature(object = "geneSet")}: ... 
\item[description] \code{signature(object = "geneSet")}: ... 
\item[description<-] \code{signature(object = "geneSet")}: ... 
\item[dominant] \code{signature(object = "geneSet")}: ... 
\item[errorMetrics] \code{signature(object = "geneSet")}: ... 
\item[errorMetrics<-] \code{signature(object = "geneSet")}: ... 
\item[genotypeLevels] \code{signature(object = "geneSet")}: ... 
\item[genotypes] \code{signature(object = "geneSet")}: ... 
\item[head] \code{signature(x = "geneSet")}: ... 
\item[heterozygote] \code{signature(object = "geneSet")}: ... 
\item[homozygote] \code{signature(object = "geneSet")}: ... 
\item[markerInfo] \code{signature(object = "geneSet")}: ... 
\item[markerInfo<-] \code{signature(object = "geneSet")}: ... 
\item[markerNames] \code{signature(object = "geneSet")}: ... 
\item[missingCodes] \code{signature(object = "geneSet")}: ... 
\item[missingCodes<-] \code{signature(object = "geneSet")}: ... 
\item[nallele] \code{signature(object = "geneSet")}: ... 
\item[nmarker] \code{signature(object = "geneSet")}: ... 
\item[nobs] \code{signature(x = "geneSet")}: ... 
\item[notes] \code{signature(object = "geneSet")}: ... 
\item[notes<-] \code{signature(object = "geneSet")}: ... 
\item[phase] \code{signature(object = "geneSet")}: ... 
\item[phase<-] \code{signature(object = "geneSet")}: ... 
\item[ploidy] \code{signature(object = "geneSet")}: ... 
\item[ploidy<-] \code{signature(object = "geneSet")}: ... 
\item[recessive] \code{signature(object = "geneSet")}: ... 
\item[sampleInfo] \code{signature(object = "geneSet")}: ... 
\item[sampleInfo<-] \code{signature(object = "geneSet")}: ... 
\item[show] \code{signature(object = "geneSet")}: ... 
\item[studyInfo] \code{signature(object = "geneSet")}: ... 
\item[studyInfo<-] \code{signature(object = "geneSet")}: ... 
\item[tail] \code{signature(x = "geneSet")}: ... 
\item[transTables] \code{signature(object = "geneSet")}: ... 
\item[transTables<-] \code{signature(object = "geneSet")}: ... 
}
\end{Section}
\begin{Note}\relax
~~further notes~~
\end{Note}
\begin{Author}\relax
J.Cheng, modified by S. Chasalow, and
Gregory R. Warnes <warnes@bst.rochester.edu>
\end{Author}
\begin{References}\relax
~put references to the literature/web site here ~
\end{References}
\begin{Examples}
\begin{ExampleCode}
##---- Should be DIRECTLY executable !! ----
\end{ExampleCode}
\end{Examples}

