ucscTrackSet-class        package:rtracklayer        R Documentation

_C_l_a_s_s "_u_c_s_c_T_r_a_c_k_S_e_t"

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

     Each track in UCSC has an associated 'ucscTrackLine' that contains
     metadata on the track.

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

     Objects can be created by calls of the form 'new("ucscTrackSet",
     assayData, phenoData, featureData, experimentData, annotation,
     ...)'. See 'trackSet' for more details.

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


     '_t_r_a_c_k_L_i_n_e': Object of class '"ucscTrackLine"' holding track
          metadata. 

     '_g_e_n_o_m_e': Object of class '"character"' identifying the genome of
          this track, e.g. "hg18".

     '_a_s_s_a_y_D_a_t_a': Object of class '"AssayData"' holding the
          experimental measurements under 'dataVals'. 

     '_p_h_e_n_o_D_a_t_a': Object of class '"AnnotatedDataFrame"' holding the
          experimental design matrix. 

     '_f_e_a_t_u_r_e_D_a_t_a': Object of class '"AnnotatedDataFrame"' holding
          feature information, generally including columns 'featChrom'
          (chromosome), 'featStart' (start position), 'featEnd' (end
          position) and 'featSTrand' (strand on the DNA: "+", "-", or
          'NA').

     '_e_x_p_e_r_i_m_e_n_t_D_a_t_a': Object of class '"MIAME"' holding experimental
          metadata. 

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"character"' referring to the
          annotation dataset. 

     '.___c_l_a_s_s_V_e_r_s_i_o_n__': Object of class '"Versions"' holding version
          information. 

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

     Class '"trackSet"', directly. Class '"eSet"', by class "trackSet",
     distance 2. Class '"VersionedBiobase"', by class "trackSet",
     distance 3. Class '"Versioned"', by class "trackSet", distance 4.

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


     '_e_x_p_o_r_t._b_e_d(_o_b_j_e_c_t, _c_o_n, _w_i_g = _F_A_L_S_E, _t_r_a_c_k_L_i_n_e =         !_w_i_g)' 
          Exports the track and its track line (if 'trackLine' is
          'TRUE') to 'con' in the Browser Extended Display (BED)
          format. 

     '_e_x_p_o_r_t._g_f_f(_o_b_j_e_c_t)' Exports the track and its track line (as a
          comment) to 'con' in the General Feature Format (GFF). 

     '_e_x_p_o_r_t._u_c_s_c(_o_b_j_e_c_t)' Exports the track and its track line to
          'con' in the UCSC meta-format.  

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

     Michael Lawrence

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

     'import' and 'export' for reading and writing tracks to and from
     connections (files), respectively.

