ucscSession-class        package:rtracklayer        R Documentation

_C_l_a_s_s "_u_c_s_c_S_e_s_s_i_o_n"

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

     An implementation of 'browserSession' for the UCSC genome browser.

_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
     'browserSession("ucsc", url = "http://genome.ucsc.edu/cgi-bin")'.

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


     '_u_r_l': Object of class '"character"' holding the base URL of the
          UCSC browser. 

     '_h_g_u_i_d': Object of class '"numeric"' holding the user
          identification code.

     '_v_i_e_w_s': Object of class '"environment"' containing a list stored
          under the name "instances". The list holds the instances of
          'browserView' for this session. 

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

     Class '"browserSession"', directly.

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


     '_b_r_o_w_s_e_r_V_i_e_w(_o_b_j_e_c_t, _s_e_g_m_e_n_t =         _g_e_n_o_m_e_S_e_g_m_e_n_t(_o_b_j_e_c_t), _t_r_a_c_k = _t_r_a_c_k_s(_o_b_j_e_c_t), ...)' 
          Creates a 'browserView' of 'segment' with visible tracks
          named in 'track'. Arguments in '...' correspond to slots in
          the 'genomeSegment' class and override those in 'segment'. 

     '_b_r_o_w_s_e_r_V_i_e_w_s'(_o_b_j_e_c_t) Gets the 'browserView' instances for this
          session. 

     '_g_e_n_o_m_e_S_e_g_m_e_n_t'(_o_b_j_e_c_t) Gets the 'genomeSegment' last displayed in
          this session. 

     '_g_e_n_o_m_e_S_e_q_u_e_n_c_e(_o_b_j_e_c_t, _s_e_g_m_e_n_t, _t_r_a_c_k = "_A_s_s_e_m_b_l_y")' Gets the
          sequence in 'segment' and 'track'.

     '_l_a_y_T_r_a_c_k(_o_b_j_e_c_t, _t_r_a_c_k, _n_a_m_e = _n_a_m_e_s(_t_r_a_c_k),         _v_i_e_w = _T_R_U_E, _f_o_r_m_a_t = "_g_f_f")' 
          Loads a track, stored under 'name' and formatted as 'format'.

     '_t_r_a_c_k_S_e_t(_o_b_j_e_c_t, _s_e_g_m_e_n_t = _g_e_n_o_m_e_S_e_g_m_e_n_t(), _n_a_m_e =         _d_e_p_a_r_s_e(_s_u_b_s_t_i_t_u_t_e(_o_b_j_e_c_t)), _f_o_r_m_a_t = "_b_e_d", _t_a_b_l_e = _N_U_L_L)' 
          Retrieves a 'trackSet' with features in 'segment' from track
          named 'name'. Some built-in tracks have multiple series, each
          stored in a separate database table. A specific table may be
          retrieved by passing its name in the 'table' parameter. The
          exported data is formatted according to 'format'.

     '_t_r_a_c_k_s'(_o_b_j_e_c_t) Gets the names of the tracks stored in the
          session. 

     '_u_c_s_c_T_r_a_c_k_M_o_d_e_s'(_o_b_j_e_c_t) Gets the default view modes for the
          tracks in the session. 

     '_u_c_s_c_T_a_b_l_e'(_o_b_j_e_c_t) Gets the database 'table' in 'segment' from
          'track' as a 'data.frame'. 

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

     Michael Lawrence

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

     'browserSession' for creating instances of this class.

