loadData             package:maigesPack             R Documentation

_L_o_a_d _c_D_N_A _m_i_c_r_o_a_r_r_a_y _d_a_t_a _t_a_b_l_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     This function loads a cDNA microarray dataset into a temporary
     'maigesPreRaw' object.

_U_s_a_g_e:

     loadData(fileConf=paste(R.home(), "library/maiges/doc/gastro/load_gastro.conf", sep="/"))

_A_r_g_u_m_e_n_t_s:

fileConf: string specifying a file name containing the parameters to
          load data. This file must contain all the information
          necessary to load the data, which are the following:

          __d_a_t_a_D_i_r_: specify a folder name containing the data files to
               be loaded. The function tests the presence or not of the
               final bar.

          __e_x_t_: string specifying the extension of the tables (if the
               _sampleFile_ below don't contain this information). You
               don't need to put the _dot_ onto string beginning, the
               function tests this automatically.

          __s_a_m_p_l_e_F_i_l_e_: string containing the file name with the
               descriptions of the biological samples hybridised,
               including  the respective intensity data files. This
               file must be  spreadsheet-like separated by tabs in a
               plain text format. The column fields *'File'* and
               *'Ref'* are mandatory (with exactly these names). The
               first one describes the files containing the numerical
               data and the second one describes the channel used to
               label the reference sample, must be 'green' or 'red' and
               they are not case sensitive.

          __d_a_t_a_s_e_t_I_d_: string with a dataset identification.

          __g_e_n_e_M_a_p_: as in _sampleFile_, this item is a character
               string giving a file name. This file must describe the
               genes on the slides. Also it must be a plain text
               spreadsheet-like separated by tabs. There are no
               mandatory field, but it is strongly recommended that you
               specify some fields containing gene names, genbank ID,
               cluster ID and gene annotations for a nice gene
               identification.

          __h_e_a_d_e_r_s_: character string (in the R format) specifying the
               column fields from data files you want to load.

          __s_k_i_p_: number of lines to be skipped in the numeric tables.

          __s_e_p_: character that separates the fields on the numeric
               tables.

          __g_r_i_d_R_: number of print tip rows inside the slide.

          __g_r_i_d_C_: number of print tip columns inside the slide.

          __p_r_i_n_t_T_i_p_R_: number of rows inside each print tip.

          __p_r_i_n_t_T_i_p_C_: number of columns inside each print tip.

          You can see an example of this configuration file in
          RHOME/library/maiges/doc/gastro/load_gastro.conf.

_D_e_t_a_i_l_s:

     This function takes the file name with initial arguments and load
     the dataset specified by this config file. It generate a
     'maigesPreRaw' object. During the process the function writes a
     file named load.out on your working folder, that is a log of the
     process, that you can check and verify if all was done correctly.
     Obviously, the parameters _dataDir_, _sampleFile_, _geneMap_,
     _sep_, _gridR_, _gridC_, _printTipR_, _printTipC_ and _headers_
     must be specified. All other parameters may be specified as NULL
     and, if so, they are ignored. It is possible to specify any fields
     that you want in the headers parameter, but it is  strongly
     recommended that you specify the fields of spot intensity and
     background for both channels and the filed giving quality weights
     for all spots.

_V_a_l_u_e:

     This function returns a 'maigesPreRaw' object containing the
     dataset loaded.

     Once an object of class 'maigesPreRaw' was generated, you may use
     the functions 'addGeneGrps' and 'addPaths' to load informaation
     about gene groups and gene networks, respectively.

_A_u_t_h_o_r(_s):

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

_E_x_a_m_p_l_e_s:

     ## Don't run because you don't have data tables.
     ## Not run: 
     gastro = loadData(fileConf="load_gastro.conf")
     ## End(Not run)

