readGmt                package:PGSEA                R Documentation

_r_e_a_d_G_m_t

_D_e_s_c_r_i_p_t_i_o_n:

     This function will read a "gmt" file into R, returning results as
     a list of SMC objects.

_U_s_a_g_e:

     readGmt(fname)

_A_r_g_u_m_e_n_t_s:

   fname: File name of concepts in .gmt format 

_D_e_t_a_i_l_s:

     The .gmt file format is a tab delimited file format used to store
     gene lists. These gene lists are stored row by row. The first
     column is the gene set name. The second column is a brief
     description, and every entry after that is a gene within that gene
     set.

_V_a_l_u_e:

     A list of SMC objects

_A_u_t_h_o_r(_s):

     Karl Dykema <karl.dykema@vai.org>

_R_e_f_e_r_e_n_c_e_s:

     <URL: http://www.broad.mit.edu/gsea/doc/data_formats.html#gmt >

_S_e_e _A_l_s_o:

     'writeGmt'

_E_x_a_m_p_l_e_s:

             datadir <- system.file("data", package = "PGSEA")
             sample <- readGmt(file.path(datadir, "sample.gmt"))
             str(sample)

