GenomeDescription-class       package:BSgenome       R Documentation

_G_e_n_o_m_e_D_e_s_c_r_i_p_t_i_o_n _o_b_j_e_c_t_s

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

     A GenomeDescription object holds the meta information describing a
     given genome.

_D_e_t_a_i_l_s:

     In general the user will not need to manipulate directly a
     GenomeDescription instance but will manipulate instead a
     higher-level object that belongs to a class containing the
     GenomeDescription class. For example the top-level object defined
     in any BSgenome data package is a BSgenome object. But because the
     BSgenome class contains the GenomeDescription class, it is also a
     GenomeDescription object and can therefore be treated as such. In
     other words all the methods described below will work on it.

_A_c_c_e_s_s_o_r _m_e_t_h_o_d_s:

     In the code snippets below, 'x' is a GenomeDescription object.


      'organism(x)': Return the target organism for this genome e.g.
          '"Homo sapiens"', '"Mus musculus"', '"Caenorhabditis
          elegans"', etc...

      'species(x)': Return the target species for this genome e.g.
          '"Human"', '"Mouse"', '"Worm"', etc...

      'provider(x)': Return the provider of this genome e.g. '"UCSC"',
          '"BDGP"', '"FlyBase"', etc...

      'providerVersion(x)': Return the provider-side version of this
          genome. For example UCSC uses versions '"hg18"', '"hg17"',
          etc... for the different Builds of the Human genome.

      'releaseDate(x)': Return the release date of this genome e.g.
          '"Mar. 2006"'.

      'releaseName(x)': Return the release name of this genome, which
          is generally made of the name of the organization who
          assembled it plus its Build version. For example, UCSC uses
          '"hg18"' for the version of the Human genome corresponding to
          the Build 36.1 from NCBI hence the release name for this
          genome is '"NCBI Build 36.1"'.


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

     H. Pages

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

     'available.genomes', BSgenome-class

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

       library(BSgenome.Celegans.UCSC.ce2)
       provider(Celegans)
       as(Celegans, "GenomeDescription")

