BrowserSession-class       package:rtracklayer       R Documentation

_C_l_a_s_s "_B_r_o_w_s_e_r_S_e_s_s_i_o_n"

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

     An object representing a genome browser session. Each session
     corresponds to a set of loaded tracks and a set of 'BrowserView'
     instances. Note that this is a virtual class; a concrete
     implementation is provided by each backend driver.

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

     A virtual Class: No objects may be created from it. See
     'browserSession' for obtaining an instance of an implementation
     for a particular genome browser.

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

     This specifies the API implemented by each browser backend. Note
     that a backend is not guaranteed to support all operations, and
     that each backend often has additional parameters for each of the
     methods. See the backend-specific documentation for more details.
     The only built-in backend is 'UCSCSession'.

     '_b_r_o_w_s_e_r_V_i_e_w(_o_b_j_e_c_t, _r_a_n_g_e =         _r_a_n_g_e(_o_b_j_e_c_t), _t_r_a_c_k = _t_r_a_c_k_N_a_m_e_s(_o_b_j_e_c_t), ...)' 
          Constructs a 'BrowserView' of 'range' for this session.

     '_b_r_o_w_s_e_r_V_i_e_w_s(_o_b_j_e_c_t, ...)' Gets the 'BrowserView' instances
          belonging to this session.

     '_a_c_t_i_v_e_V_i_e_w(_o_b_j_e_c_t, ...)' Returns the 'BrowserView' that is
          currently active in the session.

     '_r_a_n_g_e(_x, ...)' Gets the 'RangesList' representing the range of
          the genome currently displayed by the browser (i.e. the range
          shown by the active view) or a default value (possibly
          'NULL') if no views exist.

     '_g_e_t_S_e_q(_o_b_j_e_c_t, _r_a_n_g_e =         _r_a_n_g_e(_o_b_j_e_c_t), ...)' gets a
          genomic sequence of 'range' from this session.

     '_s_e_q_u_e_n_c_e(_o_b_j_e_c_t, ...) <- _v_a_l_u_e' Loads a sequence into the
          session.

     '_t_r_a_c_k(_o_b_j_e_c_t, _n_a_m_e =         _d_e_p_a_r_s_e(_s_u_b_s_t_i_t_u_t_e(_t_r_a_c_k)), _v_i_e_w = _T_R_U_E, ...) <- _v_a_l_u_e' 
          Loads one or more 'track's into the session and optionally
          open a 'view' of the track.

     '_x[[_i]] <- _v_a_l_u_e' Loads the track 'value' into session 'x', under
          the name 'i'. Shortcut to above.

     '_x$_n_a_m_e <- _v_a_l_u_e' Loads the track 'value' into session 'x', under
          the name 'name'. Shortcut to above.

     '_t_r_a_c_k(_o_b_j_e_c_t, ...)' Gets a track from a session as a
          'RangedData'.

     '_x[[_i]]' Gets the track named 'i' from session 'x'. A shortcut to
          'track'.

     '_x$_n_a_m_e' Gets the track named 'name' from session 'x'. A shortcut
          to 'track'.

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

     '_c_l_o_s_e(_c_o_n, ...)' Close this session. 

     '_s_h_o_w(_o_b_j_e_c_t, ...)' Output a textual description of this session.

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

     Michael Lawrence

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

     'browserSession' for obtaining implementations of this class for a
     particular genome browser.

