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",
     ...)'. The arguments in '...' correspond to libcurl options, see
     'getCurlHandle'. Setting these options may be useful e.g. for
     getting past a proxy.

_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, _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), ...)' 
          Creates a 'BrowserView' of 'range' with visible tracks
          specified by 'track'. 'track' may be an instance of
          'UCSCTrackModes'. Arguments in '...' should override slots in
          'range' or else match parameters to a 'ucscTrackModes' method
          for creating a 'UCSCTrackModes' instance that will override
          modes indicated by the 'track' parameter. 

     '_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. 

     '_r_a_n_g_e'(_x) Gets the 'RangesList' last displayed in this session. 

     '_g_e_n_o_m_e(_x)' Gets the genome identifier of the session, i.e.
          'genome(range(x))'.

     '_r_a_n_g_e(_x) <- _v_a_l_u_e' Sets 'value', a 'RangesList', as the range of
          session 'x'. Note that this setting only lasts until a view
          is created or manipulated. This mechanism is useful, for
          example, when treating the UCSC browser as a database, rather
          than a genome viewer.

     '_g_e_n_o_m_e(_x) <- _v_a_l_u_e' Sets the genome identifier on the range of
          session 'x'.

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

     '_t_r_a_c_k(_o_b_j_e_c_t, _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", ...) <- _v_a_l_u_e' 
          Loads a track, stored under 'name' and formatted as 'format'.
          The arguments in '...' are passed on to 'export.ucsc', so
          they could be slots in a 'TrackLine' subclass or parameters
          to pass on to the export function for 'format'.

     '_t_r_a_c_k(_o_b_j_e_c_t, _n_a_m_e, _r_a_n_g_e = _r_a_n_g_e(_o_b_j_e_c_t),         _t_a_b_l_e = _N_U_L_L)' 
          Retrieves a 'RangedData' with features in  'range' 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. See
          'tableNames' for a way to list the available tables.

     '_t_r_a_c_k_N_a_m_e_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. 

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

     Michael Lawrence

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

     'browserSession' for creating instances of this class.

