BSParams-class           package:BSgenome           R Documentation

_C_l_a_s_s "_B_S_P_a_r_a_m_s"

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

     A parameter class for representing all parameters needed for
     running the 'bsapply' method.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("BSParams",
     ...)'.

_S_l_o_t_s:


     '_X': a BSgenome object that contains chromosomes that you wish to
          apply FUN on

     '_F_U_N': the function to apply to each chromosome in the BSgenome
          object 'X'

     '_e_x_c_l_u_d_e': this is a character vector with strings that will be
          used to filter out chromosomes whose names match these
          strings.

     '_s_i_m_p_l_i_f_y': TRUE/FALSE value to indicate whether or not the
          function should try to simplify the output for you.

     '_m_a_s_k_L_i_s_t': A named logical vector of maskStates preferred when
          used with a BSGenome object.  When using the bsapply
          function, the masks will be set to the states in this vector. 

     '_m_o_t_i_f_L_i_s_t': A character vector which should contain motifs that
          the user wishes to mask from the sequence.


_M_e_t_h_o_d_s:


     '_b_s_a_p_p_l_y(_p)' Performs the function FUN using the parameters
          contained within 'BSParams'.

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

     Marc Carlson

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

     'bsapply'

