| ProjectInfo-constructor {xps} | R Documentation |
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
## 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)