\HeaderA{ProjectInfo-constructor}{Constructor for Class ProjectInfo}{ProjectInfo.Rdash.constructor}
\aliasA{ProjectInfo}{ProjectInfo-constructor}{ProjectInfo}
\keyword{manip}{ProjectInfo-constructor}
\begin{Description}\relax
Constructor for class ProjectInfo class allows to save the relevant project 
information in the \code{\LinkA{ROOT}{ROOT}} data file and in class \code{\LinkA{DataTreeSet}{DataTreeSet}}.
\end{Description}
\begin{Usage}
\begin{verbatim}
ProjectInfo(submitter      = character(),
            laboratory     = character(),
            contact        = character(),
            project        = character(),
            author         = character(),
            dataset        = character(),
            source         = character(),
            sample         = character(),
            celline        = character(),
            primarycell    = character(),
            tissue         = character(),
            biopsy         = character(),
            arraytype      = character(),
            hybridizations = character(),
            treatments     = character())
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{submitter}] \code{"character"} representing the name of the submitter.
\item[\code{laboratory}] \code{"character"} representing the laboratory of the submitter.
\item[\code{contact}] \code{"character"} representing the contact address of the submitter.
\item[\code{project}] \code{"character"} vector representing the project information.
\item[\code{author}] \code{"character"} vector representing the author information.
\item[\code{dataset}] \code{"character"} vector representing the dataset information.
\item[\code{source}] \code{"character"} vector representing the sample source information.
\item[\code{sample}] \code{"character"} vector representing the sample  information.
\item[\code{celline}] \code{"character"} vector representing the sample information for cell lines.
\item[\code{primarycell}] \code{"character"} vector representing the sample information for primary cells.
\item[\code{tissue}] \code{"character"} vector representing the sample information for tissues.
\item[\code{biopsy}] \code{"character"} vector representing the sample information for biopsies.
\item[\code{arraytype}] \code{"character"} vector representing the array information.
\item[\code{hybridizations}] \code{"character"} vector representing the hybridization information for each hybridization.
\item[\code{treatments}] \code{"character"} vector representing the treatment information for each hybridization.
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The ProjectInfo constructor allows to save the following project information in the
\code{\LinkA{ROOT}{ROOT}} data file and in class \code{\LinkA{DataTreeSet}{DataTreeSet}}:
\Tabular{lll}{
& \code{submitter}:& name of the submitter. \\
& \code{laboratory}:& laboratory of the submitter. \\
& \code{contact}:& contact address of the submitter. \\
& \code{project}:& character vector c(name,date,type,description,comments). \\
& \code{author}:& character vector c(lastname,firstname,type,company,department,email,
phone,comments).. \\
& \code{dataset}:& character vector c(name,type,sample,submitter,date,description,comments). \\
& \code{source}:& character vector c(name,type,species,subspecies,description,comments). \\
& \code{sample}:& character vector c(name,type,sex,phenotype,genotype,extraction,
isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments). \\
& \code{celline}:& character vector c(name,type,parent,atcc,modification,sex,phenotype,
genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments). \\
& \code{primarycell}:& character vector c(name,type,date,description,sex,phenotype,
genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments). \\
& \code{tissue}:& character vector c(name,type,development,morphology,disease,stage,
donorage,ageunit,status,sex,phenotype,genotype,extraction,isxenograft,xenostrain,xenosex,
xenoage,xenoageunit,comments). \\
& \code{biopsy}:& character vector c(name,type,morphology,disease,stage,donorage,ageunit,
status,sex,phenotype,genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments). \\
& \code{arraytype}:& character vector c(chipname,chiptype,description,comments). \\
& \code{hybridizations}:& vector of character vectors with each containing
c(name,type,inputname,date,preparation,protocol,repname,replica,comments). \\
& \code{treatments}:& vector of character vectors with each containing
c(name,type,concentration,concentrationunit,time,timeunit,administration,comments).
}
\end{Details}
\begin{Value}
An object of type \code{"\LinkA{ProjectInfo}{ProjectInfo.Rdash.class}"}
\end{Value}
\begin{Note}\relax
Function \code{ProjectInfo} is used as constructor for class \code{ProjectInfo} so that the
user need not know details for creating S4 classes.
\end{Note}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{SeeAlso}\relax
\code{\LinkA{ProjectInfo}{ProjectInfo.Rdash.class}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
## fill character vectors within constructor
project <- ProjectInfo(submitter="Christian", laboratory="home",contact="email",
                       project=c("TestProject","20060106","Project Type","use Test3 data for testing","my comment"),
                       hybridizations=c(c("TestA1","hyb type","TestA1.CEL",20071117,"my prep1","standard protocol","A1",1,"my comment"),
                                        c("TestA2","hyb type","TestA2.CEL",20071117,"my prep2","standard protocol","A2",1,"my comment"),
                                        c("TestB1","hyb type","TestB1.CEL",20071117,"my prep1","standard protocol","B1",2,"my comment"),
                                        c("TestB2","hyb type","TestB2.CEL",20071117,"my prep2","standard protocol","B2",2,"my comment")))
str(project)

## alternatively add character vectors as methods after creation of constructor
authorInfo(project)    <- c("Stratowa","Christian","Project Leader","Company","Dept","cstrato.at.aon.at","++43-1-1234","my comment")
datasetInfo(project)   <- c("Test3Set","MC","Tissue","Stratowa","20060106","description","my comment")
treatmentInfo(project) <- c(c("TestA1","DMSO",4.3,"mM",1.0,"hours","intravenous","my comment"),
                            c("TestA2","DMSO",4.3,"mM",8.0,"hours","intravenous","my comment"),
                            c("TestB1","DrugA2",4.3,"mM",1.0,"hours","intravenous","my comment"),
                            c("TestB2","DrugA2",4.3,"mM",8.0,"hours","intravenous","my comment"))
str(project)
\end{ExampleCode}
\end{Examples}

