clean               package:ShortRead               R Documentation

_R_e_m_o_v_e _s_e_q_u_e_n_c_e_s _w_i_t_h _a_m_b_i_g_u_o_u_s _n_u_c_l_e_o_t_i_d_e_s _f_r_o_m _s_h_o_r_t _r_e_a_d _c_l_a_s_s_e_s

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

     Short reads may contain ambiguous base calls (i.e., IUPAC symbols
     different from A, T, G, C). This generic removes all sequences
     containing 1 or more ambiguous bases.

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

     clean(object, ...)

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

  object: An object for which 'clean' methods exist; see below to
          discover these methods.

     ...: Additional arguments, perhaps used by methods.

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

     The following method is defined, in addition to methods described
     in class-specific documentation:


     _c_l_e_a_n 'signature(x = "DNAStringSet")': Remove all sequences
          containin non-base (A, C, G, T) IUPAC symbols.


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

     An instance of 'class(object)', containing only sequences with
     non-redundant nucleotides.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     showMethods('clean')

