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|IPAR)"),
     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_I_n_t_e_n_s_i_t_i_e_s 'signature(dirPath = "SolexaPath",
          pattern=character(0), run, ..., intExtension = "_int.txt",
          nseExtension = "_nse.txt", withVariability = TRUE, verbose =
          FALSE)':

          Use 'imageAnalysisPath(sp)[run]' as the directory path(s) and
          'pattern=character(0)' as the pattern for discovering Soelxa
          'intExtension' and 'nseExtension' files, returning a
          'SolexaIntensity' object containing intensities, (optionally)
          standard errors, and read (lane, tile, x, y coordinates of
          cluster) information.


     _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.

          The '...' argument may include the named argument 'as'. This
          influences the return value, as explained on the
          'readPrb,character-method' page.


     _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_Q_s_e_q 'signature(directory="SolexaPath",
          pattern=".*_qseq.txt.*", run, ...., filtered=FALSE)':

          Use 'analysisPath(dirPath)[run]' as the directory path and
          'pattern=".*_qseq.txt.*"' as the pattern for discovering read
          and quality scores in Solexa 'qseq' files. Data from _all_
          files are read into a single object; often one will want to
          specify a pattern for each lane. Details are as for
          'readQseq,character-method'.

     _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)

