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)

