readQseq              package:ShortRead              R Documentation

_R_e_a_d _S_o_l_e_x_a _q_s_e_q _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:

     'readQseq' reads all files matching 'pattern' in a directory into
     a single 'ShortReadQ'-class object. Information on machine, lane,
     tile, x, and y coordinates, filtering status, and read number are
     not returned (although filtering status can be used to selectively
     include reads as descrbied below).

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

     readQseq(dirPath, pattern = character(0), ...,
              as=c("ShortReadQ", "XDataFrame"),
              filtered=FALSE,
              verbose=FALSE)

_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 '_qseq' files to be
          summarized.

     ...: Additional argument, passed to I/O functions.

      as: 'character(1)' indicating the class of the return type.

filtered: 'logical(1)' indicating whether to include only those reads
          passing Solexa filtering?

 verbose: 'logical(1)' indicating whether to report on progress during
          evaluation.

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

     An object of class 'ShortReadQ'.

_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)
     readQseq(sp)

