%\VignetteIndexEntry{oneChannelGUI Stand Alone Functions}
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%\VignetteKeywords{one channel microarray,extended Affymetrix GUI, limma, quality control, data filtering, time course, alternative splicing}
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\begin{document}
\title{oneChannelGUI Package: Stand Alone Functions}
\author{Raffaele A Calogero}
\date{December 28, 2009}
\maketitle

\section{oneChannelGUI Stand Alone Functions}
This ection describes stand alone functions associated to oneChannelGUI package.
The stand alone package can be used outside oneChannelGUI.
\subsection{standAloneBuildingLocalAnnotation} 
The function standAloneBuildingLocalAnnotation creates gene-level annotation data using netaffx database:
\begin{Schunk}
\begin{Sinput}
> tmp <- standAloneBuildingLocalAnnotation(libDirLocation = getwd(), netaffxUser = "myemail@somewhere.org", 
+                                             netaffxUserPw = "yourpassword", whichAnnotation = "HuEx")
\end{Sinput}
\end{Schunk}
The function requires the folder where to save the annotation object, the email registered to Affymetrix netaffx web site,
the password to access to netaffx, the annotation table (HuEx, human or MoEx, mouse or RaEx, rat)
\subsection{standAloneAddingAnnotation} 
The function standAloneAddingAnnotation attaches gene-level annotation to a data frame:
\begin{Schunk}
\begin{Sinput}
> data(file="huex.annotation",package="oneChannelGUI")
> mydf <- read.table("tmpTopTable.txt", sep="\t", header=T)
> annotated.df <- standAloneAddingAnnotation(huex.annotation, mydf, ids.column = 1)
\end{Sinput}
\end{Schunk}
The function requires an annotation data frame generated with standAloneBuildingLocalAnnotation function,
a data frame containing a gene-level data of any type (it is mandatory that one of the columns contains gene-level ids) and 
the column of the data frame to be annotated containing gene-level ids
 
This funciton can be used to attach to any data frame generated, for example with limma, to attach annotation data derived 
from the latest annotation availabel on netaffx. 
 
 
\end{document}