importGeneSets          package:sigPathway          R Documentation

_I_m_p_o_r_t _g_e_n_e _s_e_t_s _s_t_o_r_e_d _i_n _G_M_T, _G_M_X, _G_R_P, _a_n_d _X_M_L _f_i_l_e _f_o_r_m_a_t_s

_D_e_s_c_r_i_p_t_i_o_n:

     Imports gene sets stored in GMT, GMX, GRP, and XML file formats
     and converts them to sigPathway's preferred format.

_U_s_a_g_e:

     importGeneSets(fileNames, verbose = TRUE)
     gmtToG(fileNames, verbose = TRUE)
     gmxToG(fileNames, verbose = TRUE)
     grpToG(fileNames, verbose = TRUE)
     xmlToG(fileNames, verbose = TRUE)

_A_r_g_u_m_e_n_t_s:

fileNames: a character vector specifying the file(s) containing the
          gene sets of interest

 verbose: a boolean to indicate whether to print debugging messages to
          the R console

_D_e_t_a_i_l_s:

     These functions read in gene sets stored in GMT, GMX, GRP, and XML
     file formats and converts them to a list format that sigPathway
     can use.  Redundant gene IDs in each gene set are removed during
     conversion.  The 'importGeneSets' function can read in GMT, GMX,
     GRP, and XML files in one pass.  The 'gmtToG', 'gmxToG', 'grpToG',
     and 'xmlToG' functions are specific to reading in their respective
     file formats.

_V_a_l_u_e:

     A list containing sublists representing each imported gene set. 
     The vignette contains more details about the list structure.

_N_o_t_e:

     These functions do not check whether the files are in the correct
     format and will give spurious output when given files in the wrong
     format.  The 'xmlToG' function requires the 'XML' package, which
     is available on CRAN.  The 'xmlToG' function also requires XML
     files to be formatted based on the MSigDB Document Type
     Definition.

_A_u_t_h_o_r(_s):

     Weil Lai

_R_e_f_e_r_e_n_c_e_s:

     <URL:
     http://www.broad.mit.edu/cancer/software/gsea/wiki/index.php/Data_formats>

