SolexaPath-class          package:ShortRead          R Documentation

"_S_o_l_e_x_a_P_a_t_h" _c_l_a_s_s _r_e_p_r_e_s_e_n_t_i_n_g _a _s_t_a_n_d_a_r_d _o_u_t_p_u_t _f_i_l_e _h_i_e_r_a_r_c_h_y

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

     Solexa produces a hierarchy of output files. The content of the
     hierarchy varies depending on analysis options. This class
     represents a standard class hierarchy, constructed by searching a 
     file hierarchy for appropriately named directories.

_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 by calls to the constructor:

     'SolexaPath(experimentPath, dataPath=.solexaPath(experimentPath,
     "Data"), scanPath=.solexaPath(dataPath, "GoldCrest"),
     imageAnalysisPath=.solexaPath(dataPath, "^C"),
     baseCallPath=.solexaPath(imageAnalysisPath, "^Bustard"),
     analysisPath=.solexaPath(baseCallPath, "^GERALD"), ...,
     verbose=FALSE) '


     _e_x_p_e_r_i_m_e_n_t_P_a_t_h 'character(1)' object pointing to the top-level
          directory of a Solexa run, e.g.,
          '/home/solexa/user/080220_HWI-EAS88_0004'. This is the only
          required argument

     _d_a_t_a_P_a_t_h (optional) Solexa Data folder .

     _s_c_a_n_P_a_t_h (optional) Solexa GoldCrest image scan path.

     _i_m_a_g_e_A_n_a_l_y_s_i_s_P_a_t_h (optional) Firecrest image analysis path.

     _b_a_s_e_C_a_l_l_P_a_t_h (optional) Bustard base call path.

     _a_n_a_l_y_s_i_s_P_a_t_h (optional) Gerald analysis pipeline path.

     ... Additional arguments, unused by currently implemented methods.

     _v_e_r_b_o_s_e=_F_A_L_S_E (optional) logical vector which, when 'TRUE' results
          in warnings if paths do not exist.

     All paths must be fully-specified.

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

     'SolexaPath' has the following slots, containing either a fully
     specified path to the corresponding directory (described above) or
     'NA' if no appropriate directory was discovered.

     '_e_x_p_e_r_i_m_e_n_t_P_a_t_h' See above.

     '_d_a_t_a_P_a_t_h' See above.

     '_s_c_a_n_P_a_t_h' See above.

     '_i_m_a_g_e_A_n_a_l_y_s_i_s_P_a_t_h' See above.

     '_b_a_s_e_C_a_l_l_P_a_t_h' See above.

     '_a_n_a_l_y_s_i_s_P_a_t_h' See above.

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

     Class '".Solexa"', directly. Class '".ShortReadBase"', by class
     ".Solexa", distance 2.

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

     Transforming methods include:


     _r_e_a_d_P_r_b 'signature(dirPath = "SolexaPath", pattern=character(0),
          run, ...)':

          Use 'baseCallPath(dirPath)[run]' as the directory path(s) and
          'pattern=character(0)' as the pattern for discovering Solexa
          prb files, retuning a 'SFastqQuality' object containing the
          maximum qualities found for each base of each cycle.

     _r_e_a_d_F_a_s_t_q 'signature(dirPath = "SolexaPath", pattern =
          ".*_sequence.txt", run, ...)':

          Use 'analysisPath(dirPath)[run]' as the directory path(s) and
          'pattern=".*_sequence.txt"' as the pattern for discovering
          fastq-formatted files, returning a 'ShortReadQ' object. Note
          that the default method reads _all_ sequence files into a
          single object; often one will want to specify a pattern for
          each lane. 

     _r_e_a_d_B_a_s_e_Q_u_a_l_i_t_y 'signature(dirPath = "SolexaPath", seqPattern =
          ".*_seq.txt", prbPattern = "s_[1-8]_prb.txt", run, ...)': 

          Use 'baseCallPath(dirPath)[run]' as the directory path(s) and
          'seqPattern=".*_seq.txt"' as the pattern for discovering base
          calls and 'prbPattern=".*_prb.txt"' as the pattern for
          discovering quality scores. Note that the default method
          reads _all_ base call and quality score files into a single
          object; often one will want to specify a pattern for each
          lane.

     _r_e_a_d_A_l_i_g_n_e_d 'signature(dirPath = "SolexaPath", pattern =
          ".*_export.txt", run, ..., filter=srFilter())': 

          Use 'analysisPath(dirPath)[run]' as the directory path and
          'pattern=".*_export.txt"' as the pattern for discovering
          Eland-aligned reads in the Solexa 'export' file format. Note
          that the default method reads _all_ aligned read files into a
          single object; often one will want to specify a pattern for
          each lane. Use an object of 'SRFilter' to select specific
          chromosomes, strands, etc.

     _q_a 'signature(dirPath="SolexaPath", pattern="character(0)", run,
          ...)':

          Use 'analysisPath(dirPath)[run]' as the directorpy path(s)
          and 'pattern=".*_export.txt"' as the pattern for discovering
          solexa 'export'-formatted fileds, returning a
          'SolexaExportQA' object summarizing quality assessment. If
          'Rmpi' has been initiated, quality assessment calculations
          are distributed across available nodes (one node per export
          file.)

     _r_e_p_o_r_t 'signature(x, ..., dest=tempfile(), type="pdf")': Use
          'qa(x, ...)' to generate quality assessment measures, and use
          these to generate a quality assessment report at location
          'dest' of type 'type' (e.g., pdf).


     _S_o_l_e_x_a_S_e_t 'signature(path = "SolexaPath")': create a 'SolexaSet'
          object based on 'path'.


     Additional methods include:


     _s_h_o_w 'signature(object = "SolexaPath")': briefly summarize the
          file paths of 'object'. The 'experimentPath' is given in
          full; the remaining paths are identified by their leading
          characters.

     _d_e_t_a_i_l 'signature(object = "SolexaPath")': summarize file paths of
          'object'. All file paths are presented in full.

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

     Martin Morgan

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

     showClass("SolexaPath")
     showMethods(class="SolexaPath")
     sf <- system.file("extdata", package="ShortRead")
     sp <- SolexaPath(sf)
     sp
     readFastq(sp, pattern="s_1_sequence.txt")
     ## Not run: 
     nfiles <- length(list.files(analysisPath(sp), "s_[1-8]_export.txt"))
     library(Rmpi)
     mpi.spawn.Rslaves(nslaves=nfiles)
     report(qa(sp))
     ## End(Not run)

