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>

