ProjectInfo-class {xps} | R Documentation

## Class ProjectInfo

### Description

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

### Objects from the Class

Objects can be created by calls of the form
`new("ProjectInfo", submitter=[character], laboratory=[character], contact=[character], ...)`.
Alternatively, the constructor `ProjectInfo` can be used.

### Slots

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

### Methods

projectInfo
  `signature(object = "ProjectInfo")`: extracts slot `project`.
projectInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `project` with character vector c(name,date,type,description,comments).
authorInfo
  `signature(object = "ProjectInfo")`: extracts slot `author`.
authorInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `author` with character vector c(lastname,firstname,type,company,department,email, phone,comments).
datasetInfo
  `signature(object = "ProjectInfo")`: extracts slot `dataset`.
datasetInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `dataset` with character vector c(name,type,sample,submitter,date,description,comments).
sourceInfo
  `signature(object = "ProjectInfo")`: extracts slot `source`.
sourceInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `source` with character vector c(name,type,species,subspecies,description,comments).
sampleInfo
  `signature(object = "ProjectInfo")`: extracts slot `sample`.
sampleInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `sample` with character vector c(name,type,sex,phenotype,genotype,extraction, isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
cellineInfo
  `signature(object = "ProjectInfo")`: extracts slot `celline`.
cellineInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `celline` with character vector c(name,type,parent,atcc,modification,sex,phenotype, genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
primcellInfo
  `signature(object = "ProjectInfo")`: extracts slot `primarycell`.
primcellInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `primarycell` with character vector c(name,type,date,description,sex,phenotype, genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
tissueInfo
  `signature(object = "ProjectInfo")`: extracts slot `tissue`.
tissueInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `tissue` with character vector c(name,type,development,morphology,disease,stage, donorage,ageunit,status,sex,phenotype,genotype,extraction,isxenograft,xenostrain,xenosex, xenoage,xenoageunit,comments).
biopsyInfo
  `signature(object = "ProjectInfo")`: extracts slot `biopsy`.
biopsyInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `biopsy` with character vector c(name,type,morphology,disease,stage,donorage,ageunit, status,sex,phenotype,genotype,extraction,isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).
arrayInfo
  `signature(object = "ProjectInfo")`: extracts slot `arraytype`.
arrayInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `arraytype` with character vector c(chipname,chiptype,description,comments).
hybridizInfo
  `signature(object = "ProjectInfo")`: extracts slot `hybridizations`.
hybridizInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `hybridizations` with vector of character vectors with each containing c(name,type,inputname,date,preparation,protocol,repname,replica,comments).
treatmentInfo
  `signature(object = "ProjectInfo")`: extracts slot `treatments`.
treatmentInfo<-
  `signature(object = "ProjectInfo", value = "character")`: replaces slot `treatments` with vector of character vectors with each containing c(name,type,concentration,concentrationunit,time,timeunit,administration,comments).
show
  `signature(object = "ProjectInfo")`: shows the content of `ProjectInfo`.

### Author(s)

Christian Stratowa

### Examples

    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)

[Package xps version 1.0.2 Index]