\HeaderA{decodeCallCodes}{Converts integer codes in a callCodes matrix to character string
representations of geneSet.}{decodeCallCodes}
\keyword{misc}{decodeCallCodes}
\begin{Description}\relax
Converts integer codes in a callCodes matrix to character string
representations of geneSet.
\end{Description}
\begin{Usage}
\begin{verbatim}
decodeCallCodes(callCodes, transTables, markerInfo)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{callCodes}] matrix of positive integers, such as the callCodes slot of
a geneSet object.

\item[\code{transTables}] list of code translation tables, such as the transTables
slot of a geneSet object.

\item[\code{markerInfo}] dataframe, with one row for each row in the callCodes
matrix, such as the markerInfo slot of a geneSet object.
Must include at least column "TransTable".

\end{ldescription}
\end{Arguments}
\begin{Value}
a character matrix with the same dimension and dimnames as
argument callCodes, giving character string representations of
genotypes, as specified by a set of translation tables.
\end{Value}
\begin{Author}\relax
Scott D. Chasalow
\end{Author}
\begin{SeeAlso}\relax
geneSet
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
library(GeneticsBase)
tTabList <- makeTransTableList(c("Bb", "ATG"), c("Generic", "SNP"))
locus <- c("c104t", "c2249t")
ttab <- c("SNP", "Generic")
minfo <- makeMarkerInfo(locus, ttab)
misscodes <- list(Generic = c("NA", ".", "-"), SNP = "N")
r1 <- c(1, 2, 1, 1)
r2 <- c(1, 2, 3, 2)
data <- rbind(r1, r2) # callCodes
dimnames(data) <- list(locus, paste("Sample", seq(along = r1),
        sep = "."))
decodeCallCodes(data, tTabList, minfo)
\end{ExampleCode}
\end{Examples}

