RochePath-class          package:ShortRead          R Documentation

"_R_o_c_h_e_P_a_t_h" _c_l_a_s_s _r_e_p_r_e_s_e_n_t_i_n_g _a _R_o_c_h_e (_4_5_4) _e_x_p_e_r_i_m_e_n_t _l_o_c_a_t_i_o_n

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

     This class represents the directory location where Roche (454)
     result files (fasta sequences) can be found.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects from the class are created with the 'RocehPath'
     constructor:

     'RochePath(experimentPath = NA_character_, readPath =
     .srPath(experimentPath, "run"), qualPath = readPath, ..., verbose
     = FALSE) '



     _e_x_p_e_r_i_m_e_n_t_P_a_t_h 'character(1)' or 'RochePath' pointing to the
          top-level directory of a Roche experiment.

     _r_e_a_d_P_a_t_h 'character()' of directories (typically in
          'experimentPath') containing sequence (read) information. The
          default selects all directories matching
          'list.files(experimentPath, "run")'.

     _q_u_a_l_P_a_t_h 'character()' of directories (typically in
          'experimentPath') containing quality information. The default
          selects all directories matching 'list.files(experimentPath,
          "run")'.

     _v_e_r_b_o_s_e 'logical(1)' indicating whether invalid paths should be
          reported interactively.


_S_l_o_t_s:

     'RocheSet' has the following slots:


     '_r_e_a_d_P_a_t_h': Object of class '"character"', as described in the
          constructor, above.

     '_q_u_a_l_P_a_t_h': Object of class '"character"', as described in the
          constructor, above.

     '_b_a_s_e_P_a_t_h': Object of class '"character"', containing the
          'experimentPath'.


_E_x_t_e_n_d_s:

     Class '"ExperimentPath"', directly. Class '".Roche"', directly.
     Class '".ShortReadBase"', by class "ExperimentPath", distance 2.
     Class '".ShortReadBase"', by class ".Roche", distance 2.

_M_e_t_h_o_d_s:

     'RochePath' has the following methods or functions defined:

     _r_e_a_d_F_a_s_t_a 'signature(dirPath = "character", pattern=".\.fna$",
          sample = 1,  ...)':

     _r_e_a_d_F_a_s_t_a 'signature(dirPath = "RochePath", pattern=".\.fna$",
          sample = 1, run, ...)': 

          Read sequences from files matching 'list.files(dirPath,
          pattern)' (when 'dirPath="character"') or
          'list.files(readPath(dir)[run], pattern)', retaining reads
          corresponding to 'sample'. The result is a 'DNAStringSet'.

     _r_e_a_d_Q_u_a_l 'signature(dirPath = "RochePath", pattern="\.qual$",
          reads=NULL, sample=1, run, ...)': 

          Read quality scores from files matching
          'list.files(qualPath(dirPath)[run])', corresponding to
          'sample'. Non-null 'reads' is used as an (optional) template
          for parsing quality scores. 

     _r_e_a_d_4_5_4 'signature(dirPath = "RochePath")': read sequences and
          quality scores into a 'ShortReadQ'.

     _r_e_a_d_P_a_t_h 'signature(object = "RochePath")': return the contents of
          the 'readPath' slot.

     _r_u_n_N_a_m_e_s 'signature(object = "RochePath")': return the 'basename's
          of 'readPath(object)'.

     _R_o_c_h_e_S_e_t 'signature(path = "RochePath")': create a 'RocheSet' from
          'path'.


     Additional methods include:


     _s_h_o_w 'signature(object = "RochePath")': Briefly summarize the
          experiment path locations.

     _d_e_t_a_i_l 'signature(object = "RochePath")': Provide additional
          detail on the Roche path. All file paths are presented in
          full.

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

     Michael Lawrence <mflawrence@fhcrc.org>

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

     'ExperimentPath'.

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

     showClass("RochePath")

