addPaths             package:maigesPack             R Documentation

_F_u_n_c_t_i_o_n _t_o _l_o_a_d _g_e_n_e _p_a_t_h_w_a_y_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 gene
     pathways in TGF format. This format must have the genes of the
     pathway sequentially in lines numbered from 1, followed by a '#'
     character that separate the nodes (given by genes) from edges,
     that must be specified as number of the origin gene followed by a
     space, the number of the final gene, another space and the weight
     of the iteration. This function stores the gene networks read in
     the slot 'Paths' into objects of class 'maigesPreRaw'.

_U_s_a_g_e:

     addPaths(data, folder="./", ext=".tgf")

_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 '.tgf'.
          The function also tests the presence of the initial dot.

_D_e_t_a_i_l_s:

     If the 'data' object already has gene networks with names equal to
     some someones that are been read, the nets 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 pathway
     of interest. These files must be done in TGF format, as described
     into description above. The gene identification are matched with
     some column from 'genemap' (see 'loadData').

_V_a_l_u_e:

     This function return another object of class 'maigesPreRaw', with
     the slot 'Paths' actualised.

_A_u_t_h_o_r(_s):

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

_S_e_e _A_l_s_o:

     'maigesPreRaw', 'addGeneGrps'

_E_x_a_m_p_l_e_s:

     ## Don't run because you don't have the pathways in a readable folder.
     ## Not run: 
     gastro = addPaths(gastro, folder="geneNets", ext="tgf")
     ## End(Not run)

