readBaseQuality          package:ShortRead          R Documentation

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

     'readBaseQuality' reads all base call files in a directory
     'dirPath' whose file name matches 'seqPattern' and all quality
     score files whose name matches 'prbPattern', returning a compact
     internal representation of the sequences, and quality scores in
     the files. Methods read all files into a single R object.

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

     readBaseQuality(dirPath, seqPattern=character(0), prbPattern=character(0), ...)

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

 dirPath: A character vector (or other object; see methods defined on
          this generic) giving the directory path (relative or
          absolute) of files to be input.

seqPattern: The ('grep'-style) pattern describing base call file names
          to be read. The default ('character(0)') results in
          (attempted) input of all files in the directory.

prbPattern: The ('grep'-style) pattern describing quality score file
          names to be read. The default ('character(0)') results in
          (attempted) input of all files in the directory.

     ...: Additional arguments, perhaps used by methods.

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

     A single R object (e.g., 'ShortReadQ') containing sequences and
     qualities of all files in 'dirPath' matching 'seqPattern' and
     'prbPattern' respectively. There is no guarantee of order in which
     files are read.

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

     Patrick Aboyoun <paboyoun@fhcrc.org>

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

     A 'ShortReadQ' object.

     'readXStringColumns', 'readPrb'

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

     sp <- SolexaPath(system.file("extdata", package="ShortRead"))
     readBaseQuality(sp, seqPattern="s_1.*_seq.txt", prbPattern="s_1.*_prb.txt")

