\HeaderA{simplifyGateNames}{Standardize flow cytometry gate names}{simplifyGateNames}
\aliasA{simplifyGateNames,character-method}{simplifyGateNames}{simplifyGateNames,character.Rdash.method}
\aliasA{simplifyGateNames,filter-method}{simplifyGateNames}{simplifyGateNames,filter.Rdash.method}
\keyword{methods}{simplifyGateNames}
\keyword{list}{simplifyGateNames}
\begin{Description}\relax
This function helps to standardize typical flow cytometry cell population names. This is useful when trying to combine the results from a large number of flow runs wherein the cytometrist may have used slightly different nomenclature to describe the same set of cells.   For example, "Lymphocytes" vs. "lymphoctes".
\end{Description}
\begin{Usage}
\begin{verbatim} 
simplifyGateNames(x, ...) 
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{x}] Logical.  Default=FALSE.  A flowCore style filter, or a text string with a gate (filter) name 
\item[\code{...}] Additional arguments:    
\emph{upperCaseGates} Logical.  Default=FALSE.  If TRUE, convert the gate names to all upper case    \\
\emph{stripFileName}  Logical.  Default=TRUE.  It is currently the convention that the flowFlowJo code prepends the name of the referenced FCS file within the gate name, followed by a colon, then the rest of the gate information.  This setting looks for ".*\bsl{}.fcs:" and strips it out of the gate name   \\ 
\emph{removeParentalNames} Logical.  Default=TRUE.  The current \emph{getFlowJoGates} method concatenates a gate's name with the name of all of it's parents.  \\ 

\end{ldescription}
\end{Arguments}
\begin{Value}
This function returns either a text string or flowCore style filter object.
\end{Value}
\begin{Author}\relax
John Gosink
\end{Author}
\begin{Examples}
\begin{ExampleCode} 
simplifyGateNames(c("LymphoCytes", "lymphocytes", "mOnOcYtEs"));
simplifyGateNames(c("Lymphocytes:CD8+"), removeParentalNames=TRUE); 
simplifyGateNames("CD34 positive cells ") 
simplifyGateNames("CD34 + ") 
\end{ExampleCode}
\end{Examples}

