genomeSegment-methods      package:rtracklayer      R Documentation

_A_c_c_e_s_s_i_n_g _a _s_e_g_m_e_n_t _o_f _a _g_e_n_o_m_e

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

     Methods for creating, getting or setting a 'genomeSegment'.

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

     The following methods are defined by 'rtracklayer'.



     _o_b_j_e_c_t = "_c_h_a_r_a_c_t_e_r" 'genomeSegment(object, chrom = character(0),
          start = character(0), end = character(0), segment =
          genomeSegment())': Create a 'genomeSegment' instance with the
          same slot values as 'segment', except where overriden by one
          of the other parameters, which all correspond to slots in
          'genomeSegment'. Note that 'object' corresponds to the
          'genome' slot.


     _o_b_j_e_c_t = "_m_i_s_s_i_n_g" 'genomeSegment(object, genome = character(0),
          chrom = character(0), start = character(0), end =
          character(0), segment = new("genomeSegment"))': Similar to
          above, except 'object' is omitted and 'genome' is an explicit
          parameter.


     _o_b_j_e_c_t = "_t_r_a_c_k_S_e_t" Get the segment spanned by a track. 

     _o_b_j_e_c_t = "_t_r_a_c_k_S_e_t_s" Get the union (including gaps) of spans for
          all tracks. 

     _o_b_j_e_c_t = "_b_r_o_w_s_e_r_S_e_s_s_i_o_n" Get the current segment (i.e. segment
          displayed by active view or default segment). 

     _o_b_j_e_c_t = "_u_c_s_c_S_e_s_s_i_o_n" Get the last accessed segment. 

     _o_b_j_e_c_t = "_u_c_s_c_V_i_e_w" _o_r "_a_r_g_o_V_i_e_w" 'genomeSegment(object)': Get the
          segment displayed by the view.

          'genomeSegment(object) <- value': Set the segment displayed
          by the the view.


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

       ## Create a genome segment for genome "hg18", chromosome 22
       genomeSegment("hg18", "chr22")
       ## Explicitly specify parameters
       segment <- genomeSegment(genome = "hg18", chrom = "chr22", start = 150000)
       ## Add an 'end' value
       genomeSegment(end = 200000, segment = segment)

