\HeaderA{ProjectInfo-class}{Class ProjectInfo}{ProjectInfo.Rdash.class}
\aliasA{arrayInfo}{ProjectInfo-class}{arrayInfo}
\aliasA{arrayInfo,ProjectInfo-method}{ProjectInfo-class}{arrayInfo,ProjectInfo.Rdash.method}
\aliasA{arrayInfo<\Rdash}{ProjectInfo-class}{arrayInfo<.Rdash.}
\aliasA{arrayInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{arrayInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{authorInfo}{ProjectInfo-class}{authorInfo}
\aliasA{authorInfo,ProjectInfo-method}{ProjectInfo-class}{authorInfo,ProjectInfo.Rdash.method}
\aliasA{authorInfo<\Rdash}{ProjectInfo-class}{authorInfo<.Rdash.}
\aliasA{authorInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{authorInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{biopsyInfo}{ProjectInfo-class}{biopsyInfo}
\aliasA{biopsyInfo,ProjectInfo-method}{ProjectInfo-class}{biopsyInfo,ProjectInfo.Rdash.method}
\aliasA{biopsyInfo<\Rdash}{ProjectInfo-class}{biopsyInfo<.Rdash.}
\aliasA{biopsyInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{biopsyInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{cellineInfo}{ProjectInfo-class}{cellineInfo}
\aliasA{cellineInfo,ProjectInfo-method}{ProjectInfo-class}{cellineInfo,ProjectInfo.Rdash.method}
\aliasA{cellineInfo<\Rdash}{ProjectInfo-class}{cellineInfo<.Rdash.}
\aliasA{cellineInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{cellineInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{datasetInfo}{ProjectInfo-class}{datasetInfo}
\aliasA{datasetInfo,ProjectInfo-method}{ProjectInfo-class}{datasetInfo,ProjectInfo.Rdash.method}
\aliasA{datasetInfo<\Rdash}{ProjectInfo-class}{datasetInfo<.Rdash.}
\aliasA{datasetInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{datasetInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{hybridizInfo}{ProjectInfo-class}{hybridizInfo}
\aliasA{hybridizInfo,ProjectInfo-method}{ProjectInfo-class}{hybridizInfo,ProjectInfo.Rdash.method}
\aliasA{hybridizInfo<\Rdash}{ProjectInfo-class}{hybridizInfo<.Rdash.}
\aliasA{hybridizInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{hybridizInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{primcellInfo}{ProjectInfo-class}{primcellInfo}
\aliasA{primcellInfo,ProjectInfo-method}{ProjectInfo-class}{primcellInfo,ProjectInfo.Rdash.method}
\aliasA{primcellInfo<\Rdash}{ProjectInfo-class}{primcellInfo<.Rdash.}
\aliasA{primcellInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{primcellInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{projectInfo}{ProjectInfo-class}{projectInfo}
\aliasA{projectInfo,ProjectInfo-method}{ProjectInfo-class}{projectInfo,ProjectInfo.Rdash.method}
\aliasA{projectInfo<\Rdash}{ProjectInfo-class}{projectInfo<.Rdash.}
\aliasA{projectInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{projectInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{sampleInfo}{ProjectInfo-class}{sampleInfo}
\aliasA{sampleInfo,ProjectInfo-method}{ProjectInfo-class}{sampleInfo,ProjectInfo.Rdash.method}
\aliasA{sampleInfo<\Rdash}{ProjectInfo-class}{sampleInfo<.Rdash.}
\aliasA{sampleInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{sampleInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{show,ProjectInfo-method}{ProjectInfo-class}{show,ProjectInfo.Rdash.method}
\aliasA{sourceInfo}{ProjectInfo-class}{sourceInfo}
\aliasA{sourceInfo,ProjectInfo-method}{ProjectInfo-class}{sourceInfo,ProjectInfo.Rdash.method}
\aliasA{sourceInfo<\Rdash}{ProjectInfo-class}{sourceInfo<.Rdash.}
\aliasA{sourceInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{sourceInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{tissueInfo}{ProjectInfo-class}{tissueInfo}
\aliasA{tissueInfo,ProjectInfo-method}{ProjectInfo-class}{tissueInfo,ProjectInfo.Rdash.method}
\aliasA{tissueInfo<\Rdash}{ProjectInfo-class}{tissueInfo<.Rdash.}
\aliasA{tissueInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{tissueInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\aliasA{treatmentInfo}{ProjectInfo-class}{treatmentInfo}
\aliasA{treatmentInfo,ProjectInfo-method}{ProjectInfo-class}{treatmentInfo,ProjectInfo.Rdash.method}
\aliasA{treatmentInfo<\Rdash}{ProjectInfo-class}{treatmentInfo<.Rdash.}
\aliasA{treatmentInfo<-,ProjectInfo,character-method}{ProjectInfo-class}{treatmentInfo<.Rdash.,ProjectInfo,character.Rdash.method}
\keyword{classes}{ProjectInfo-class}
\begin{Description}\relax
This 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{Section}{Objects from the Class}
Objects can be created by calls of the form \\
\code{new("ProjectInfo", submitter=[character], laboratory=[character], contact=[character], ...)}. \\
Alternatively, the constructor \code{\LinkA{ProjectInfo}{ProjectInfo}} can be used.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{submitter}:] Object of class \code{"character"} representing the name of the submitter.
\item[\code{laboratory}:] Object of class \code{"character"} representing the laboratory of the submitter.
\item[\code{contact}:] Object of class \code{"character"} representing the contact address of the submitter.
\item[\code{project}:] Object of class \code{"list"} representing the project information.
\item[\code{author}:] Object of class \code{"list"} representing the author information.
\item[\code{dataset}:] Object of class \code{"list"} representing the dataset information.
\item[\code{source}:] Object of class \code{"list"} representing the sample source information.
\item[\code{sample}:] Object of class \code{"list"} representing the sample  information.
\item[\code{celline}:] Object of class \code{"list"} representing the sample information for cell lines.
\item[\code{primarycell}:] Object of class \code{"list"} representing the sample information for primary cells.
\item[\code{tissue}:] Object of class \code{"list"} representing the sample information for tissues.
\item[\code{biopsy}:] Object of class \code{"list"} representing the sample information for biopsies.
\item[\code{arraytype}:] Object of class \code{"list"} representing the array information.
\item[\code{hybridizations}:] Object of class \code{"data.frame"} representing the hybridization information for each hybridization.
\item[\code{treatments}:] Object of class \code{"data.frame"} representing the treatment information for each hybridization.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[projectInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{project}.
\item[projectInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{project} with character vector c(name,date,type,description,comments).
\item[authorInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{author}.
\item[authorInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{author} with character vector c(lastname,firstname,type,company,department,email,
phone,comments).
\item[datasetInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{dataset}.
\item[datasetInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{dataset} with character vector c(name,type,sample,submitter,date,description,comments).
\item[sourceInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{source}.
\item[sourceInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{source} with character vector c(name,type,species,subspecies,description,comments).
\item[sampleInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{sample}.
\item[sampleInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{sample} with character vector c(name,type,sex,phenotype,genotype,extraction,
isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
\item[cellineInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{celline}.
\item[cellineInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{celline} with character vector c(name,type,parent,atcc,modification,sex,phenotype,
genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
\item[primcellInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{primarycell}.
\item[primcellInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{primarycell} with character vector c(name,type,date,description,sex,phenotype,
genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
\item[tissueInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{tissue}.
\item[tissueInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{tissue} with character vector c(name,type,development,morphology,disease,stage,
donorage,ageunit,status,sex,phenotype,genotype,extraction,isxenograft,xenostrain,xenosex,
xenoage,xenoageunit,comments).
\item[biopsyInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{biopsy}.
\item[biopsyInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{biopsy} with character vector c(name,type,morphology,disease,stage,donorage,ageunit,
status,sex,phenotype,genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
\item[arrayInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{arraytype}.
\item[arrayInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{arraytype} with character vector c(chipname,chiptype,description,comments).
\item[hybridizInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{hybridizations}.
\item[hybridizInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{hybridizations} with vector of character vectors with each containing
c(name,type,inputname,date,preparation,protocol,repname,replica,comments).
\item[treatmentInfo] \code{signature(object = "ProjectInfo")}: extracts slot \code{treatments}.
\item[treatmentInfo<-] \code{signature(object = "ProjectInfo", value = "character")}: replaces 
slot \code{treatments} with vector of character vectors with each containing
c(name,type,concentration,concentrationunit,time,timeunit,administration,comments).
\item[show] \code{signature(object = "ProjectInfo")}: shows the content of \code{ProjectInfo}.
}
\end{Section}
\begin{Author}\relax
Christian Stratowa
\end{Author}
\begin{Examples}
\begin{ExampleCode}
project <- new("ProjectInfo",submitter="Christian", laboratory="home",contact="email")
projectInfo(project)    <- c("TestProject","20060106","Project Type","use Test3 data for testing","my comment")
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")
sourceInfo(project)     <- c("Unknown","source type","Homo sapiens","caucasian","description","my comment")
primcellInfo(project)   <- c("Mel31","primary cell",20071123,"extracted from patient","male","my pheno","my genotype","RNA extraction",TRUE,"NMRI","female",7.0,"months", "my comment")
arrayInfo(project)      <- c("Test3","GeneChip","description","my comment")
hybridizInfo(project)   <- 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"))
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"))
show(project)
\end{ExampleCode}
\end{Examples}

