SRFilter-class           package:ShortRead           R Documentation

"_S_R_F_i_l_t_e_r" _f_o_r _r_e_p_r_e_s_e_n_t_i_n_g _f_u_n_c_t_i_o_n_s _o_p_e_r_a_t_i_n_g _o_n _S_h_o_r_t_R_e_a_d _o_b_j_e_c_t_s

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

     Objects of this class are functions that, when provided an
     appropriate object from the ShortRead package, return logical
     vectors indicating which parts of the object satisfy the filter
     criterion.

     A number of filters are built-in (described below); users are free
     to create their own filters, using the 'srFilter' function.

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

     Objects can be created through 'srFilter' (to create a
     user-defined filter) or through calls to constructors for
     predefined filters, as described on the 'srFilter' page.

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



     '._D_a_t_a': Object of class '"function"' taking a single named
          argument 'x' corresponding to the ShortRead object that the
          filter will be applied to. The return value of the filter
          function is expected to be a logical vector that can be used
          to subset 'x' to include those elements of 'x' satisfying the
          filter.


     '_n_a_m_e': Object of class '"ScalarCharacter"' representing the name
          of the filter. The name is useful for suggesting the purpose
          of the filter, and for debugging failed filters.


_E_x_t_e_n_d_s:

     Class '"function"', from data part. Class '".SRUtil"', directly.
     Class '"OptionalFunction"', by class "function", distance 2. Class
     '"PossibleMethod"', by class "function", distance 2.

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



     _s_r_F_i_l_t_e_r 'signature(fun = "SRFilter")': Return the function
          representing the underlying filter; this is primarily for
          interactive use to understanding filter function; usually the
          filter is invoked as a normal function call, as illustrated
          below


     _n_a_m_e 'signature(x = "SRFilter")': Return, as a 'ScalarCharacter',
          the name of the function.


     _s_h_o_w 'signature(object = "SRFilter")': display a brief summary of
          the filter


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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'srFilter' for predefined and user-defined filters.

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

     ## see ?srFilter

