aGFFCalc-class             package:ACME             R Documentation

_C_l_a_s_s "_a_G_F_F_C_a_l_c"

_D_e_s_c_r_i_p_t_i_o_n:

     Store results of ACME calculations

_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("aGFFCalc",
     ...)'.

_S_l_o_t_s:

     '_c_a_l_l': Object of class '"call"', contains the exact call to
          do.aGFF.calc, for historical purposes

     '_t_h_r_e_s_h_o_l_d': Object of class '"numeric"', the threshold used in
          the calculation

     '_c_u_t_p_o_i_n_t_s': Object of class '"numeric"', the data value above
          which probes were considered positive

     '_v_a_l_s': Object of class '"matrix"', equivalent in size to the
          original data matrix, containing the calculated p-values from
          the ACME algorithm

     '_a_n_n_o_t_a_t_i_o_n': Object of class '"data.frame"', currently a copy of
          the original annotation, possibly reordered in chromosome
          order 

     '_d_a_t_a': Object of class '"matrix"', the original data, possibly
          reordered

     '_s_a_m_p_l_e_s': Object of class '"data.frame"', sample metadata

_E_x_t_e_n_d_s:

     Class '"aGFF"', directly.

_M_e_t_h_o_d_s:

     _p_l_o_t 'signature(x = "aGFFCalc", ask=FALSE)': plot the results of
          an ACME calculation

     _p_r_i_n_t 'signature(x = "aGFFCalc")': brief overview of the object

     _s_h_o_w 'signature(object = "aGFFCalc")': brief overview of the
          object

_A_u_t_h_o_r(_s):

     Sean Davis <sdavis2@mail.nih.gov>

_S_e_e _A_l_s_o:

     'do.aGFF.calc', 'aGFF-class'

_E_x_a_m_p_l_e_s:

     data(example.agff)
     example.agffcalc <- do.aGFF.calc(example.agff,window=1000,thresh=0.9)
     example.agffcalc

