aGFF-class               package:ACME               R Documentation

_C_l_a_s_s _f_o_r _s_t_o_r_i_n_g _G_F_F-_l_i_k_e _d_a_t_a

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

     The GFF format is quite versatile while remaining simple. This
     class simply stores the annotation associated with a set of GFF
     files from the same regions of the genome along with some
     information about the samples from which the data came and the
     data (from the "score" column of the GFF file) themselves.

_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 'new("aGFF", ...). 
     Also, the \code{read.resultsGFF()} function returns aGFF
     objects.'.

_S_l_o_t_s:

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"data.frame"' with two columns
          absolutely necessary, "Chromosome" and "Location". Other
          columns can be included.

     '_d_a_t_a': Object of class '"matrix"' of the same number of rows as
          the annotation slot and the same number of columns as the
          number of rows in the samples slot, containing data for later
          analysis

     '_s_a_m_p_l_e_s': Object of class '"data.frame"' for describing the
          samples, one row per sample

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

     _p_l_o_t 'signature(x = "aGFF")': to plot a region along the genome.

     _p_r_i_n_t 'signature(x = "aGFF")': simple method to display summary of
          aGFF object

     _s_h_o_w 'signature(object = "aGFF")': simple method to display
          summary of aGFF object

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

     Sean Davis

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

     'read.resultsGFF' and'aGFFCalc-class'

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

     # Load an example
     data(example.agff)
     example.agff

