ProjectInfo-constructor         package:xps         R Documentation

_C_o_n_s_t_r_u_c_t_o_r _f_o_r _C_l_a_s_s _P_r_o_j_e_c_t_I_n_f_o

_D_e_s_c_r_i_p_t_i_o_n:

     Constructor for class ProjectInfo class allows to save the
     relevant project  information in the 'ROOT' data file and in class
     'DataTreeSet'.

_U_s_a_g_e:

     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())

_A_r_g_u_m_e_n_t_s:

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.

_D_e_t_a_i_l_s:

     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).

_V_a_l_u_e:

     An object of type '"ProjectInfo"'

_N_o_t_e:

     Function 'ProjectInfo' is used as constructor for class
     'ProjectInfo' so that the user need not know details for creating
     S4 classes.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_S_e_e _A_l_s_o:

     'ProjectInfo'

_E_x_a_m_p_l_e_s:

     ## 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)

