utilities              package:EBarrays              R Documentation

_U_t_i_l_i_t_y _f_u_n_c_t_i_o_n_s _f_o_r _t_h_e _E_B_a_r_r_a_y_s _p_a_c_k_a_g_e

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

     Utilitiy functions for the EBarrays package

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

     createExprSet(datafile, repfile)
     ebPatterns(x)

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

datafile: file with data

 repfile: file with replication information

       x: x can be a character vector (of length > 2) (see example), or
          an arbitrary connection which should provide patterns, one
          line for each pattern. If 'x' is a character vector of length
          1, it is assumed to be the name of a file (since there's no
          point in a patterns object with only one pattern) which is
          then opened and treated as a connection. 

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

     'ebPatterns' creates objects that represent a collection of
     hypotheses to be used by 'emfit'.

     It, along with 'createExprSet', also provides back compatibility
     with an earlier version of 'EBarrays', which required input data
     to be in a very specific format. For example, the (earlier) usage
     'cleanup(NULL, "data.txt", "repfile.txt", "patternfile.txt")' can
     be replaced by 'createExprSet("data.txt", "repfile.txt")' and
     'ebPatterns("patternfile.txt")'.

     Unless one has data in this particular format, the 'createExprSet'
     function can be safely ignored.

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

     'createExprSet' creates an object of class '"exprSet"'.

     'ebPatterns' creates an Object of class ``ebarraysPatterns'', to
     be used in other functions such as 'emfit'. This is nothing more
     than a list (and can be treated as such as far as indexing goes)
     and is used only for method dispatch.

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

     Christina Kendziorski, Michael Newton and Deepayan Sarkar

_S_e_e _A_l_s_o:

     'emfit'

_E_x_a_m_p_l_e_s:

     patterns <- ebPatterns(c("1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1",
                              "1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2"))
     show(patterns)

