BCRANKsearch-class          package:BCRANK          R Documentation

_C_l_a_s_s "_B_C_R_A_N_K_s_e_a_r_c_h"

_D_e_s_c_r_i_p_t_i_o_n:

     Holds the whole search path from a single 'bcrank' run. Each
     individual search step is stored in a 'BCRANKmatch-class' object. 
     Several objects of this class are collected in a
     'BCRANKresult-class' object

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects are not intended to be created directly but as a result
     from running 'bcrank'.

_S_l_o_t_s:


     '_s_e_a_r_c_h_P_a_t_h': a collection of 'BCRANKmatch-class' objects,
          ontaining all bcrank search steps from a start guess to a
          locally optimal solution.

     '_f_i_n_a_l_P_W_M': position weight matrix containing all DNA sites for
          the highest scoring consensus in this bcrank run.

_M_e_t_h_o_d_s:


     _s_e_a_r_c_h_P_a_t_h 'signature(object = "BCRANKsearch", i=NULL)': If 'i' is
          NULL, returns a data frame containing consensus and score for
          the whole search path. Otherwise, the i'th
          'BCRANKmatch-class' object in the search path is returned.

     _p_w_m 'signature(object = "BCRANKsearch", normalize=TRUE)': Returns
          the position weight matrix (pwm) for the highest scoring
          consensus in this bcrank run. Matrix positions are between
          between 0 and 1 when 'normalize' is TRUE. When FALSE, the
          number of matching sequences is reported.  

     _p_l_o_t 'signature(x = "BCRANKsearch", y = "missing")': A plot method
          for the searchPath.

_A_u_t_h_o_r(_s):

     Adam Ameur, adam.ameur@lcb.uu.se

_S_e_e _A_l_s_o:

     'bcrank', 'BCRANKmatch-class', 'BCRANKresult-class'

