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

