ProjectInfo-constructor {xps} | R Documentation

## Constructor for Class ProjectInfo

### Description

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

### Usage

    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())

### Arguments

`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.

### Details

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).

### Value

An object of type `"ProjectInfo"`

### Note

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

### Author(s)

Christian Stratowa

### See Also

`ProjectInfo`

### Examples

    ## 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)

[Package xps version 1.4.10 Index]