ucscTrackModes-methods      package:rtracklayer      R Documentation

_A_c_c_e_s_s_i_n_g _U_C_S_C _t_r_a_c_k _m_o_d_e_s

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

     Generics for getting and setting UCSC track visibility modes
     ("hide", "dense", "full", "pack", "squish").

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


          The following methods are defined by 'rtracklayer' for
          *getting* the track modes through the generic
          'ucscTrackModes(object, ...)'.

     _o_b_j_e_c_t = "_c_h_a_r_a_c_t_e_r" 'function(object, hide = character(), dense =
          character(), pack = character(), squish = character(), full =
          character())' Creates an instance of 'UCSCTrackModes' from
          'object', a character vector of mode names, with the
          corresponding track names given in the 'names' attribute.
          Note that 'object' can be a 'UCSCTrackModes' instance. The
          other parameters are character vectors naming the tracks for
          each mode and overriding the modes specified by 'object'.


     _o_b_j_e_c_t = "_m_i_s_s_i_n_g" The same interface as above, except 'object'
          defaults to an empty character vector.


     _o_b_j_e_c_t = "_U_C_S_C_V_i_e_w" Gets modes for tracks in the view.


     _o_b_j_e_c_t = "_U_C_S_C_S_e_s_s_i_o_n" Gets default modes for the tracks in the
          session. These are the modes that will be used as the default
          for a newly created view.

          The following methods are defined by 'rtracklayer' for
          *setting* the track modes through the generic
          'ucscTrackModes(object) <- value'.

     _o_b_j_e_c_t = "_U_C_S_C_V_i_e_w", _v_a_l_u_e = "_U_C_S_C_T_r_a_c_k_M_o_d_e_s" Sets the modes for
          the tracks in the view.


     _o_b_j_e_c_t = "_U_C_S_C_V_i_e_w", _v_a_l_u_e = "_c_h_a_r_a_c_t_e_r" Sets the modes from a
          character vector of mode names, with the corresponding track
          names given in the 'names' attribute.


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

     'trackNames' and 'trackNames<-' for just getting or setting which
     tracks are visible (not of mode "hide").

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

     # Tracks "foo" and "bar" are fully shown, "baz" is hidden
     modes <- ucscTrackModes(full = c("foo", "bar"), hide = "baz")
     # Update the modes to hide track "bar"
     modes2 <- ucscTrackModes(modes, hide = "bar")

