| ProjectInfo-class {xps} | R Documentation |
This class allows to save the relevant project information in the
ROOT data file and in class DataTreeSet.
Objects can be created by calls of the form
new("ProjectInfo", submitter=[character], laboratory=[character], contact=[character], ...).
Alternatively, the constructor ProjectInfo can be used.
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:"list" representing the project information.author:"list" representing the author information.dataset:"list" representing the dataset information.source:"list" representing the sample source information.sample:"list" representing the sample information.celline:"list" representing the sample information for cell lines.primarycell:"list" representing the sample information for primary cells.tissue:"list" representing the sample information for tissues.biopsy:"list" representing the sample information for biopsies.arraytype:"list" representing the array information.hybridizations:"data.frame" representing the hybridization information for each hybridization.treatments:"data.frame" representing the treatment information for each hybridization.signature(object = "ProjectInfo"): extracts slot project.signature(object = "ProjectInfo", value = "character"): replaces
slot project with character vector c(name,date,type,description,comments).signature(object = "ProjectInfo"): extracts slot author.signature(object = "ProjectInfo", value = "character"): replaces
slot author with character vector c(lastname,firstname,type,company,department,email,
phone,comments).signature(object = "ProjectInfo"): extracts slot dataset.signature(object = "ProjectInfo", value = "character"): replaces
slot dataset with character vector c(name,type,sample,submitter,date,description,comments).signature(object = "ProjectInfo"): extracts slot source.signature(object = "ProjectInfo", value = "character"): replaces
slot source with character vector c(name,type,species,subspecies,description,comments).signature(object = "ProjectInfo"): extracts slot sample.signature(object = "ProjectInfo", value = "character"): replaces
slot sample with character vector c(name,type,sex,phenotype,genotype,extraction,
isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).signature(object = "ProjectInfo"): extracts slot celline.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).signature(object = "ProjectInfo"): extracts slot primarycell.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).signature(object = "ProjectInfo"): extracts slot tissue.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).signature(object = "ProjectInfo"): extracts slot biopsy.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).signature(object = "ProjectInfo"): extracts slot arraytype.signature(object = "ProjectInfo", value = "character"): replaces
slot arraytype with character vector c(chipname,chiptype,description,comments).signature(object = "ProjectInfo"): extracts slot hybridizations.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).signature(object = "ProjectInfo"): extracts slot treatments.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).signature(object = "ProjectInfo"): shows the content of ProjectInfo.Christian Stratowa
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)