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 of class 'SFastqQuality'. Methods do this by identifying
     the maximum base call quality for each cycle and read, and
     representing this as an ASCII-encoded character string following
     Solexa conventions.

_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.

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

     An object of class 'SFastqQuality'

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     ~~objects to See Also as 'help', ~~~

_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

