UCSCData-class          package:rtracklayer          R Documentation

_C_l_a_s_s "_U_C_S_C_D_a_t_a"

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

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

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


     '_t_r_a_c_k_L_i_n_e': Object of class '"TrackLine"' 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 'chrom'
          (chromosome), 'start' (start position), 'end' (end position)
          and 'strand' (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. 

_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_s(_o_b_j_e_c_t, "_U_C_S_C_D_a_t_a")' Constructs a 'UCSCData' from a
          'RangedData' instance, by adding a default track line and
          ensuring that the sequence/chromosome names are compliant
          with UCSC conventions.


_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.

