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)