addGeneGrps            package:maigesPack            R Documentation

_F_u_n_c_t_i_o_n _t_o _l_o_a_d _g_e_n_e _g_r_o_u_p_s _i_n_t_o _m_a_i_g_e_s_P_r_e_R_a_w _o_b_j_e_c_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function read a directory and read files containing the genes
     for specific gene groups. This files must have one gene per line.
     This function stores the gene groups read in the slot 'GeneGrps'
     into objects of class 'maigesPreRaw'.

_U_s_a_g_e:

     addGeneGrps(data, folder="./", ext=".txt")

_A_r_g_u_m_e_n_t_s:

    data: object of 'maigesPreRaw' class.

  folder: char string specifying the directory of gene groups. The
          function tests the presence or not of the final bar.

     ext: string giving the extension of the files, defaults to '.txt'.
          The function also tests the presence of the initial dot.

_D_e_t_a_i_l_s:

     If the 'data' object already has gene groups with names equal to
     some someones that are been read, the groups with repeated names
     are not added. Warning messages are printed for every repeated
     group name.

     The 'folder' directory must contain only one file for each gene
     group of interest. These files must discriminate one gene per
     line. The identification of the genes must be done by one of the
     gene labels given by 'genemap' (see 'loadData').

_V_a_l_u_e:

     This function returns another object of class 'maigesPreRaw', with
     the slot 'GeneGroups' actualised.

_A_u_t_h_o_r(_s):

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

_S_e_e _A_l_s_o:

     'maigesPreRaw', 'addPaths'

_E_x_a_m_p_l_e_s:

     ## Don't run because you don't have the gene sets in a readable folder.
     ## Not run: 
     gastro = addGeneGrps(gastro, folder="geneGrps", ext="txt")
     ## End(Not run)

