report               package:ShortRead               R Documentation

_S_u_m_m_a_r_i_z_e _q_u_a_l_i_t_y _a_s_s_e_s_s_m_e_n_t _r_e_s_u_l_t_s _i_n_t_o _a _r_e_p_o_r_t

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

     This generic function summarizes results from evaluation of 'qa'
     into a report. Available report formats vary depending on the data
     analysed.

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

     report(x, ..., dest=tempfile(), type="html")

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

       x: An object returned by 'qa', usually derived from class '.QA'

     ...: Additional arguments used by specific methods. See specific
          methods for details.

    dest: The output destination for the final report. For
          'type="html"' this is a directory; for (deprecated)
          'type="pdf"' this is a file.

    type: A text string defining the type of report; available report
          types depend on the type of object 'x'; usually this is
          html.

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

     The following methods are defined:


   '_x="_B_o_w_t_i_e_Q_A", ..., _d_e_s_t=_t_e_m_p_f_i_l_e(), _t_y_p_e="_h_t_m_l"' Produce an
        HTML-based report from an object of class 'BowtieQA'.

   '_x="_F_a_s_t_q_Q_A", ..., _d_e_s_t=_t_e_m_p_f_i_l_e(), _t_y_p_e="_h_t_m_l"' Produce an
        HTML-based report from an object of class 'FastqQA'.


   '_x="_M_A_Q_M_a_p_Q_A", ..., _d_e_s_t=_t_e_m_p_f_i_l_e(), _t_y_p_e="_h_t_m_l"' Produce an
        HTML-based report from an object of class 'MAQMapQA'.


   '_x="_S_o_l_e_x_a_E_x_p_o_r_t_Q_A", ..., _d_e_s_t=_t_e_m_p_f_i_l_e(), _t_y_p_e="_h_t_m_l"' Produce an
        HTML-based report from an object of class 'SolexaExportQA'.


   '_x="_S_o_l_e_x_a_E_x_p_o_r_t_Q_A", ..., _d_e_s_t=_t_e_m_p_f_i_l_e(), _t_y_p_e="_p_d_f"' (Deprecated)
        Produce an PDF report from an object of class 'SolexaExportQA'.


   '_x="_S_o_l_e_x_a_P_a_t_h", ..., _d_e_s_t=_t_e_m_p_f_i_l_e(), _t_y_p_e="_h_t_m_l"' Produce an HTML
        report by first visiting all '_export.txt' files in the
        'analysisPath' directory of 'x' to create a 'SolexaExportQA'
        instance.


   '_x="_S_o_l_e_x_a_P_a_t_h", ..., _d_e_s_t=_t_e_m_p_f_i_l_e(), _t_y_p_e="_p_d_f"' (Deprecated)
        Produce an PDF report by first visiting all '_export.txt' files
        in the 'analysisPath' directory of 'x' to create a
        'SolexaExportQA' instance.


    '_x="_A_N_Y", ..., _d_e_s_t=_t_e_m_p_f_i_l_e(), _t_y_p_e="_A_N_Y"'  This method is used
        internally

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

     This function is invoked for its side effect;  the return value is
     the name of the directory or file where the report was created.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'SolexaExportQA'

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

     showMethods("report")

