maigesPreRaw-class        package:maigesPack        R Documentation

_m_a_i_g_e_s_P_r_e_R_a_w _c_l_a_s_s, _s_t_o_r_e _p_r_e _r_a_w _m_i_c_r_o_a_r_r_a_y _d_a_t_a_s_e_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     This class describes objects to handle data values and information
     about genes and samples used in the data. Here, it is possible to
     put any field from data tables that you want.

_D_e_t_a_i_l_s:

     This class of objects is intended to define an intermediate step
     between the external world (data tables, gene groups, gene
     networks, etc) and real raw objects given by the class
     'maigesRaw'. In this intermediate step the user can do any type of
     exploratory analysis and set bad spots (at slot 'BadSpots'), or to
     do any type of calculation they judge important in the fields of
     'Data' slot.

     This class of objects is created by a call from 'loadData'. The
     functions 'addGeneGrps' and 'addPaths' may also be used to add
     information for gene groups and gene networks. After the
     exploratory analysis it must be converted in an object of class
     'maigesRaw' using the function 'createMaigesRaw'.

     If you have the package _Rgraphviz_ installed and working it is
     possible to display the graphs stored in the slot 'Paths' using
     the command 'plot'.

_S_l_o_t_s:


     '_D_a_t_a': contains a list with matrices. Each matrix has 'nrow' =
          number of spots and 'ncol' = number of data tables (or chips)
          with the numerical values of each data field specified by the
          user in the configuration file used as parameter for
          'loadData' function.

     '_G_e_n_e_G_r_p_s': a list containing character vectors. These vectors
          specify genes from the gene groups that must be studied. Each
          vector is used as a gene group. The names of the groups are
          catch from the names of the vectors from the list, that is
          catch from file names.

     '_P_a_t_h_s': list containing 'graphNEL' objects specifying gene
          regulatory networks (or pathways). As in the previous slot,
          the names are catch from file names and stored as names of
          the elements from the list.

     '_L_a_y_o_u_t': a list containing the number of rows ('gridR') and
          columns ('gridC') of grids, the number of rows ('spotR') and
          columns ('spotC') of spots inside each grid and the total
          number of spots.

     '_G_l_a_b_e_l_s': data frame giving the gene labels. These labels are
          generally used during the data analysis.

     '_S_l_a_b_e_l_s': data frame giving the sample labels. These labels are
          generally used during the data analysis.

     '_B_a_d_S_p_o_t_s': logical vector specifying spots that was judged as bad
          ones. By default this slot is created as a vector of FALSEs
          with same length as number of spots.

     '_N_o_t_e_s': char string that receives any comment about the dataset.
          The dataset description is stored in this slot.

     '_D_a_t_e': char string giving the date and hour that the object was
          created.

     '_V._i_n_f_o': list containg three characters. The first one is a
          string containing the R version used when the object was
          created. The second is a char vector with base packages and
          the last one is another char vector with additional packages
          and version numbers.

_M_e_t_h_o_d_s:


     _p_r_i_n_t 'signature(x = 'maigesPreRaw')': print method for
          'maigesPreRaw' class.

     _s_h_o_w 'signature(x = 'maigesPreRaw')': show method for
          'maigesPreRaw' class.

     _s_u_m_m_a_r_y 'signature(x = 'maigesPreRaw')': summary method for
          'maigesPreRaw' class.

_A_u_t_h_o_r(_s):

     Gustavo H. Esteves <gesteves@vision.ime.usp.br>

_S_e_e _A_l_s_o:

     'loadData', 'addGeneGrps', 'addPaths', 'createMaigesRaw'.

