qa                 package:ShortRead                 R Documentation

_P_e_r_f_o_r_m _q_u_a_l_i_t_y _a_s_s_e_s_s_m_e_n_t _o_n _s_h_o_r_t _r_e_a_d_s

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

     This function is a common interface to quality assessment
     functions available in 'ShortRead'. Results from this function may
     be displayed in brief, or integrated into reports using, e.g.,
     'report'.

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

     qa(dirPath, ...)

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

 dirPath: A character vector or other object (e.g., 'SolexaPath'; see
          'showMethods', below) locating the data for which quality
          assessment is to be performed. See help pages for defined
          methods (by evaluating the example code, below) for details
          of available methods.

     ...: Additional arguments used by methods.

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

     The following methods are defined:

    '_d_i_r_P_a_t_h="_c_h_a_r_a_c_t_e_r", _p_a_t_t_e_r_n="_c_h_a_r_a_c_t_e_r",                 _t_y_p_e=_c("_S_o_l_e_x_a_E_x_p_o_r_t", "_B_o_w_t_i_e", "_M_A_Q_M_a_p_S_h_o_r_t", "_f_a_s_t_q"), ...' 
        Quality assessment is performed on all files in directory
        'dirPath' whose file name matches 'pattern'. The type of
        analysis performed is based on the 'type' argument. Use
        'SolexaExport' when all files matching 'pattern' are Solexa
        '_export.txt' files. Use 'Bowtie' for Bowtie files. Use
        'MAQMapShort' for MAQ 'map' files produced by MAQ versions
        below 0.70, and 'fastq' for collections of fastq-format files.
        Quality assessment details vary depending on data source.


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

     An object derived from class '.QA'

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     '.QA', 'SolexaExportQA' 'MAQMapQA' 'FastqQA'

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

     showMethods("qa")

