readPrb              package:ShortRead              R Documentation

_R_e_a_d _S_o_l_e_x_a _p_r_b _f_i_l_e_s _a_s _f_a_s_t_q-_s_t_y_l_e _q_u_a_l_i_t_y _s_c_o_r_e_s

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

     'readPrb' reads all '_prb.txt' files in a directory into a single
     object. Most methods (see details) do this by identifying the
     maximum base call quality for each cycle and read, and
     representing this as an ASCII-encoded character string.

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

     readPrb(dirPath, pattern = character(0), ...)

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

 dirPath: Directory path or other object (e.g., 'SolexaPath' for which
          methods are defined.

 pattern: Regular expression matching names of '_prb' files to be
          summarized.

     ...: Additional arguments, e.g., to 'srapply', used during
          evaluation.

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

     The 'readPrb,character-method' contains an arugment 'as' that
     determines the value of the returned object, as follows.



   '_a_s="_S_o_l_e_x_a_E_n_c_o_d_i_n_g"' The ASCII encoding of the maximum per cycle
        and read quality score is encoded using Solexa conventions.


   '_a_s="_F_a_s_t_q_E_n_c_o_d_i_n_g"' The ASCII encoding of the maximum per cycle and
        read quality score is encoded using Fastq conventions, i.e.,
        '!' has value 0.


   '_a_s="_I_n_t_g_e_r_E_n_c_o_d_i_n_g"' The maximum per cycle and read quality score
        is returned as a in integer value. Values are collated into a
        matrix with number of rows equal to number of reads, and number
        of columns equal to number of cycles.


   '_a_s="_a_r_r_a_y"' The quality scores are _not_ summarized; the return
        value is an integer array with dimensions corresponding to
        reads, nucleotids, and cycles.



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

     An object of class 'QualityScore', or an integer matrix.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     fl <- system.file("extdata", package="ShortRead")
     sp <- SolexaPath(fl)
     readPrb(sp, "s_1.*_prb.txt") # all tiles to a single file

