ProjectInfo-constructor: Constructor for Class ProjectInfo
In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description Usage Arguments Details Value Note Author(s) See Also Examples

Constructor for class ProjectInfo class allows to save the relevant project information in the ROOT data file and in class DataTreeSet.

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())

`submitter`	`"character"` representing the name of the submitter.
`laboratory`	`"character"` representing the laboratory of the submitter.
`contact`	`"character"` representing the contact address of the submitter.
`project`	`"character"` vector representing the project information.
`author`	`"character"` vector representing the author information.
`dataset`	`"character"` vector representing the dataset information.
`source`	`"character"` vector representing the sample source information.
`sample`	`"character"` vector representing the sample information.
`celline`	`"character"` vector representing the sample information for cell lines.
`primarycell`	`"character"` vector representing the sample information for primary cells.
`tissue`	`"character"` vector representing the sample information for tissues.
`biopsy`	`"character"` vector representing the sample information for biopsies.
`arraytype`	`"character"` vector representing the array information.
`hybridizations`	`"character"` vector representing the hybridization information for each hybridization.
`treatments`	`"character"` vector representing the treatment information for each hybridization.

The ProjectInfo constructor allows to save the following project information in the ROOT data file and in class DataTreeSet:

	`submitter`:	name of the submitter.
	`laboratory`:	laboratory of the submitter.
	`contact`:	contact address of the submitter.
	`project`:	character vector c(name,date,type,description,comments).
	`author`:	character vector c(lastname,firstname,type,company,department,email, phone,comments)..
	`dataset`:	character vector c(name,type,sample,submitter,date,description,comments).
	`source`:	character vector c(name,type,species,subspecies,description,comments).
	`sample`:	character vector c(name,type,sex,phenotype,genotype,extraction, isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
	`celline`:	character vector c(name,type,parent,atcc,modification,sex,phenotype, genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
	`primarycell`:	character vector c(name,type,date,description,sex,phenotype, genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
	`tissue`:	character vector c(name,type,development,morphology,disease,stage, donorage,ageunit,status,sex,phenotype,genotype,extraction,isxenograft,xenostrain,xenosex, xenoage,xenoageunit,comments).
	`biopsy`:	character vector c(name,type,morphology,disease,stage,donorage,ageunit, status,sex,phenotype,genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
	`arraytype`:	character vector c(chipname,chiptype,description,comments).
	`hybridizations`:	vector of character vectors with each containing c(name,type,inputname,date,preparation,protocol,repname,replica,comments).
	`treatments`:	vector of character vectors with each containing c(name,type,concentration,concentrationunit,time,timeunit,administration,comments).

An object of type "ProjectInfo"

Function ProjectInfo is used as constructor for class ProjectInfo so that the user need not know details for creating S4 classes.

Christian Stratowa

ProjectInfo

## 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)