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)