ProjectInfo-class: Class ProjectInfo

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

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)

xps documentation built on Nov. 8, 2020, 6 p.m.