ProjectInfo-class            package:xps            R Documentation

_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:

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

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 
      'new("ProjectInfo", submitter=[character],
     laboratory=[character], contact=[character], ...)'. 
      Alternatively, the constructor 'ProjectInfo' can be used.

_S_l_o_t_s:


     '_s_u_b_m_i_t_t_e_r': Object of class '"character"' representing the name
          of the submitter.

     '_l_a_b_o_r_a_t_o_r_y': Object of class '"character"' representing the
          laboratory of the submitter.

     '_c_o_n_t_a_c_t': Object of class '"character"' representing the contact
          address of the submitter.

     '_p_r_o_j_e_c_t': Object of class '"list"' representing the project
          information.

     '_a_u_t_h_o_r': Object of class '"list"' representing the author
          information.

     '_d_a_t_a_s_e_t': Object of class '"list"' representing the dataset
          information.

     '_s_o_u_r_c_e': Object of class '"list"' representing the sample source
          information.

     '_s_a_m_p_l_e': Object of class '"list"' representing the sample 
          information.

     '_c_e_l_l_i_n_e': Object of class '"list"' representing the sample
          information for cell lines.

     '_p_r_i_m_a_r_y_c_e_l_l': Object of class '"list"' representing the sample
          information for primary cells.

     '_t_i_s_s_u_e': Object of class '"list"' representing the sample
          information for tissues.

     '_b_i_o_p_s_y': Object of class '"list"' representing the sample
          information for biopsies.

     '_a_r_r_a_y_t_y_p_e': Object of class '"list"' representing the array
          information.

     '_h_y_b_r_i_d_i_z_a_t_i_o_n_s': Object of class '"data.frame"' representing the
          hybridization information for each hybridization.

     '_t_r_e_a_t_m_e_n_t_s': Object of class '"data.frame"' representing the
          treatment information for each hybridization.

_M_e_t_h_o_d_s:


     _p_r_o_j_e_c_t_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'project'.

     _p_r_o_j_e_c_t_I_n_f_o<- 'signature(object = "ProjectInfo", value =
          "character")': replaces  slot 'project' with character vector
          c(name,date,type,description,comments).

     _a_u_t_h_o_r_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'author'.

     _a_u_t_h_o_r_I_n_f_o<- 'signature(object = "ProjectInfo", value =
          "character")': replaces  slot 'author' with character vector
          c(lastname,firstname,type,company,department,email,
          phone,comments).

     _d_a_t_a_s_e_t_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'dataset'.

     _d_a_t_a_s_e_t_I_n_f_o<- 'signature(object = "ProjectInfo", value =
          "character")': replaces  slot 'dataset' with character vector
          c(name,type,sample,submitter,date,description,comments).

     _s_o_u_r_c_e_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'source'.

     _s_o_u_r_c_e_I_n_f_o<- 'signature(object = "ProjectInfo", value =
          "character")': replaces  slot 'source' with character vector
          c(name,type,species,subspecies,description,comments).

     _s_a_m_p_l_e_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'sample'.

     _s_a_m_p_l_e_I_n_f_o<- 'signature(object = "ProjectInfo", value =
          "character")': replaces  slot 'sample' with character vector
          c(name,type,sex,phenotype,genotype,extraction,
          isxenograft,xenostrain,xenosex,xenoage,xenoageunit,comments).

     _c_e_l_l_i_n_e_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'celline'.

     _c_e_l_l_i_n_e_I_n_f_o<- '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).

     _p_r_i_m_c_e_l_l_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'primarycell'.

     _p_r_i_m_c_e_l_l_I_n_f_o<- '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).

     _t_i_s_s_u_e_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'tissue'.

     _t_i_s_s_u_e_I_n_f_o<- '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).

     _b_i_o_p_s_y_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'biopsy'.

     _b_i_o_p_s_y_I_n_f_o<- '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).

     _a_r_r_a_y_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'arraytype'.

     _a_r_r_a_y_I_n_f_o<- 'signature(object = "ProjectInfo", value =
          "character")': replaces  slot 'arraytype' with character
          vector c(chipname,chiptype,description,comments).

     _h_y_b_r_i_d_i_z_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'hybridizations'.

     _h_y_b_r_i_d_i_z_I_n_f_o<- '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).

     _t_r_e_a_t_m_e_n_t_I_n_f_o 'signature(object = "ProjectInfo")': extracts slot
          'treatments'.

     _t_r_e_a_t_m_e_n_t_I_n_f_o<- '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).

     _s_h_o_w 'signature(object = "ProjectInfo")': shows the content of
          'ProjectInfo'.

_A_u_t_h_o_r(_s):

     Christian Stratowa

_E_x_a_m_p_l_e_s:

     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)

