trackSet-methods         package:rtracklayer         R Documentation

_G_e_t _a _t_r_a_c_k_S_e_t

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

     Methods for getting a 'trackSet'.

_U_s_a_g_e:

     trackSet(object, ...)

_A_r_g_u_m_e_n_t_s:

  object: An object from which to obtain a 'trackSet'.

     ...: Arguments passed on to methods.

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


          The following methods are defined by 'rtracklayer'.

     _o_b_j_e_c_t = "_A_n_n_o_t_a_t_e_d_D_a_t_a_F_r_a_m_e" 'trackSet(object, dataVals = NULL,
          ...)': A constructor that sets 'object' directly as the
          'featureData' slot and 'dataVals' into the 'dataVals' slot,
          if non-'NULL'. The arguments in '...' should correspond to
          slots in the 'trackSet' class.

     _o_b_j_e_c_t = "_d_a_t_a._f_r_a_m_e" 'trackSet(object, dataVals = NULL, ...)':
          coerces 'object' to 'AnnotatedDataFrame' and delegates to it.


     _o_b_j_e_c_t = "_I_R_a_n_g_e_s" 'trackSet(object, chrom, strand = NA, dataVals
          = NULL, ...)': Constructor that takes the start and end of
          each feature from 'object'. The chromsome, strand, data
          values and other slots are specified by 'chrom', 'strand',
          'dataVals' and '...', respectively.


     _o_b_j_e_c_t = "_c_h_a_r_a_c_t_e_r" 'trackSet(object, start = 1, end = start +
          span - 1, strand = NA, span = 1, dataVals = NULL, breaks =
          NULL, ...)': a constructor that takes 'object' to be the
          chromosome values. 'start', 'end', 'strand' and 'dataVals'
          specify the starts, ends, strands and data values,
          respectively, of the features. 'span', if given, should be a
          scalar integer indicating widths of the features If 'end' is
          specified with 'span', it must be length one and then the
          region from 'start' to 'end' is broken up into features of
          width 'span'. If 'breaks' is specified, 'span' must be
          omitted and 'start' and 'end' must be scalars. Then the
          features are formed by breaking the region from 'start' to
          'end' at the positions specified in 'breaks'. Way too
          complicated for its own good.


     _o_b_j_e_c_t = "_u_c_s_c_S_e_s_s_i_o_n" 'trackSet(object, name, segment =
          genomeSegment(object), format = "bed", table = NULL)': Get a
          track from the session by its 'name' in format 'format'. Some
          built-in tracks have multiple series, each identified by a
          'table' name.


     _o_b_j_e_c_t = "_a_r_g_o_S_e_s_s_i_o_n" 'trackSet(object, name, segment =
          genomeSegment(object))': Get a track from the session by its
          'name'.


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

     'layTrack' for loading a 'trackSet' into a session.

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

     ## Not run: 
     session <- browseGenome()
     track <- import(system.file("tests", "v1.gff", package = "rtracklayer"))
     session <- layTrack(session, track, "My Track", format = "gff1", view = TRUE)
     track <- trackSet(session, name = "My Track")
     ## End(Not run)

