SolexaSet-class          package:ShortRead          R Documentation

"_S_o_l_e_x_a_S_e_t" _c_o_o_r_d_i_n_a_t_i_n_g _S_o_l_e_x_a _o_u_t_p_u_t _l_o_c_a_t_i_o_n_s _w_i_t_h _s_a_m_p_l_e _a_n_n_o_t_a_t_i_o_n_s

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

     This class coordinates the file hierarchy produced by the Solexa
     `pipeline' with annotation data contained in an
     'AnnotatedDataFrame' (defined in the 'Biobase' package).

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

     Objects can be created from the constructor:

     'SolexaSet(path, ...)'.


     _p_a_t_h A 'character(1)' vector giving the fully-qualified path to
          the root of the directory hierarchy associated with each
          Solexa flow cell, or an object of class 'SolexaPath' (see
          'SolexaPath' for this method).

     ... Additional arguments, especially 'laneDescription', an
          'AnnotatedDataFrame' describing the content of each of the 8
          lanes in the Solexa flow cell.


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

     'SolexaSet' has the following slots:

     '_s_o_l_e_x_a_P_a_t_h': Object of class '"SolexaPath"'.

     '_l_a_n_e_D_e_s_c_r_i_p_t_i_o_n': Object of class '"AnnotatedDataFrame"',
          containing information about the samples in each lane of the
          flow cell.

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

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

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



     _s_o_l_e_x_a_P_a_t_h 'signature(object = "SolexaSet")': Return the directory
          paths present when this object was created as a 'SolexaPath'.

     _l_a_n_e_N_a_m_e_s 'signature(object = "SolexaSet")': Return the names of
          each lane in the flow cell, currently names are simply '1:8'. 

     _s_h_o_w 'signature(object = "SolexaSet")': Briefly summarize the
          experiment path and lane description of the Solexa set. 

     _d_e_t_a_i_l 'signature(object = "SolexaSet")': Provide additional
          detail on the Solexa set, including the content of
          'solexaPath' and the 'pData' and 'varMetadata' of
          'laneDescription'.


     Methods transforming 'SolexaSet' objects include:

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

          Use 'analysisPath(solexaPath(dirPath))[run]' as the directory
          path(s) 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.


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

     Martin Morgan

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

     showClass("SolexaSet")
     showMethods(class="SolexaSet")
     ## construct a SolexaSet
     sf <- system.file("extdata", package="ShortRead")
     df <- data.frame(Sample=c("Sample 1", "Sample 2", "Sample 3", "Sample
                               4", "Center-wide control", "Sample 6", "Sample
                               7", "Sample 8"),
                      Genome=c(rep("hg18", 4), "phi_plus_SNPs.txt",
                               rep("hg18", 3)))
     dfMeta <- data.frame(labelDescription=c("Type of sample",
                                             "Alignment genome"))
     adf <- new("AnnotatedDataFrame", data=df, varMetadata=dfMeta)
     SolexaSet(sf, adf)

