ShortReadQ-class          package:ShortRead          R Documentation

"_S_h_o_r_t_R_e_a_d_Q" _c_l_a_s_s _f_o_r _s_h_o_r_t _r_e_a_d_s _a_n_d _t_h_e_i_r _q_u_a_l_i_t_y _s_c_o_r_e_s

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

     This class provides a way to store and manipulate, in a
     coordinated fashion, the reads, identifiers, and quality scores of
     uniform-length short reads.

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

     Objects from this class are not normally created directly by the
     user, but are instead the result of 'readFastq'.

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

     Slots 'sread' and 'id' are inherited from 'ShortRead'. An
     additional slot defined in this class is:

     '_q_u_a_l_i_t_y': Object of class '"BStringSet"' representing a quality
          score (see 'readFastq' for some discussion of quality score).

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

     Class '"ShortRead"', directly. Class '".ShortReadBase"', by class
     "ShortRead", distance 2.

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

     See 'accessors' for additional functions to access slot content,
     and 'ShortRead' for inherited methods. Additional methods include:



     [ 'signature(x = "ShortReadQ", i = "ANY", j = "missing")':  This
          method creates a new 'ShortReadQ' object containing only
          those reads indexed by 'i'. Additional methods on
          [,ShortRead do not provide additional functionality, but
          are present to limit inappropriate use.

     _a_l_p_h_a_b_e_t_B_y_C_y_c_l_e 'signature(stringSet = "ShortReadQ")': Apply
          'alphabetByCycle' to the 'sread' component, the 'quality'
          component, and the combination of these two components of
          'stringSet', returning a list of matrices with three
          elements: '"sread"', '"quality"', and '"both"'.

     _a_l_p_h_a_b_e_t_S_c_o_r_e 'signature(object = "ShortReadQ")': See
          'alphabetScore' for details.

     _d_e_t_a_i_l 'signature(object = "ShortReadQ")': display the first and
          last entries of each of 'sread', 'id', and 'quality' entries
          of 'object'.

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

     Martin Morgan

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

     'readFastq' for creation of objects of this class from
     fastq-format files.

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

     showClass("ShortReadQ")
     showMethods(class="ShortReadQ", inherit=FALSE)
     showMethods(class="ShortRead", inherit=FALSE)

