\HeaderA{convertSmc}{Convert Entrez ID based "smc" object}{convertSmc}
\keyword{manip}{convertSmc}
\begin{Description}\relax
This function will convert the Entrez IDs of an smc object to the corresponding Entrez IDs from a different species.
Data from the homologene project is downloaded and used within this function.
\end{Description}
\begin{Usage}
\begin{verbatim}
convertSmc(mcs, fromSpecies = "h", toSpecies = "r",hgX="./homologene.data")
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{mcs}] a list of "smc" objects
\item[\code{fromSpecies}] character - a single letter describing the species to convert from ie, h=human, r= rat, etc..
\item[\code{toSpecies}] character - a single letter describing the species to convert to ie, h=human, r= rat, etc.. 
\item[\code{hgX}] character - file name of homologene data file 
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
This function will not work if you have not downloaded the homologene data file. Please use this command to do so:
download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")
\end{Details}
\begin{Value}
a list of converted "smc" objects
\end{Value}
\begin{Author}\relax
Karl Dykema <karl.dykema@vai.org>
\end{Author}
\begin{Examples}
\begin{ExampleCode}

## Not run: 
        download.file("ftp://ftp.ncbi.nih.gov/pub/HomoloGene/current/homologene.data",destfile="homologene.data",mode="wb")
        
        datadir <- system.file("data", package = "PGSEA")
        sample <- readGmt(file.path(datadir, "sample.gmt"))
        
        converted <- convertSmc(sample[1:2],"h","r")
        str(converted)
## End(Not run)

\end{ExampleCode}
\end{Examples}

