intInfo-class             package:cosmo             R Documentation

_C_l_a_s_s "_i_n_t_I_n_f_o" ~~~

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

     An object of class '"intInfo"' contains all the constraints one
     wishes to impose on an interval of the motif.   Combined
     '"intInfo"' objects will constitue an object of class
     '"constraintSet"'

_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('intInfo','
      '    constraintID      = ...., # Object of class
     \code{"numeric"}'
      '    intervalID        = ...., # Object of class
     \code{"numeric"}'
      '    type              = ...., # Object of class
     \code{"character"}'
      '    length            = ...., # Object of class
     \code{"numeric"}'
      '    prop              = ...., # Object of class
     \code{"numeric"}'
      '    boundedCon        = ...., # Object of class
     \code{"data.frame"}'
      '    posFreqConCon     = ...., # Object of class
     \code{"data.frame"}'
      '    shapeCon          = ...., # Object of class
     \code{"data.frame"}'
      '    objectCall        = ...., # Object of class \code{"call"}'
      '  )'

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


     '_c_o_n_s_t_r_a_i_n_t_I_D': Object of class '"numeric"', indicating which
          constraint set the interval is part of    

     '_i_n_t_e_r_v_a_l_I_D': Object of class '"numeric"', indicating the order of
          the interval in the constraint set    

     '_t_y_p_e': Object of class '"character"', the interval type: 'B' for
          base pairs, 'P' for proportion, or 'V' for variable

     '_l_e_n_g_t_h': Object of class '"numeric"', the length of the interval:
          if the interval is of type 'B', the length is the number of
          base pairs, if the       interval is of type 'P' or 'V', this
          slot is NA    

     '_p_r_o_p': Object of class '"numeric"', the ratio of the interval
          lengtb to the total motif width. This slot is only defined
          for intervals of type 'P', in which case       the value is
          between 0 and 100%. For intervals of type 'B' or 'V', this
          slot is NA    

     '_b_o_u_n_d_e_d_C_o_n': Object of class '"data.frame"' a data frame
          summarizing the information content bounding constraints on
          the interval: the first column indicates the position of the
          interval among the intervals constituing the constraint set,
          the second and third column are respetively the lower and
          upper bound of the information content on the interval.

     '_p_o_s_F_r_e_q_C_o_n': Object of class '"data.frame"' a data frame
          summarizing the position nucleotide frequency constraints
          imposed on the interval: the first column indicates the
          interval to which the constraint is applied, the second
          column the position concerned ('All' cab be specified if the
          constraint applies to the entire interval). It is to be noted
          that a specific position mat only be specified if the
          interval is of type 'B'. The third column is the nucleotide
          concerned, either A, C, G, T, AT, or GC are accepted at this
          time. Finally the fourth column indicates the lower bound for
          the given nucleotide at the given position.     

     '_s_h_a_p_e_C_o_n': Object of class '"data.frame"' a data frame
          summarizing the shape constraint on the interval. The first
          column indicates the interval to which the constraint is
          applied, the second the shape of the variation either
          'linear', 'monotone decreasing', or 'monotone increasing'.
          The third and fourth column (respectively fifth and sixth)
          record the lower and upper bounds of the information content
          at the beginning (respectively end) of the interval. Finally,
          the seventh column records the error tolerated.    

     '_o_b_j_e_c_t_C_a_l_l': Object of class '"call"' stores how the object was
          created     

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


     _p_l_o_t 'signature(x = "intInfo", varLen=4, propLen=4, plot.IC=TRUE,
          plot.nucFreq=TRUE)': plots the '"intInfo"' object. varLen and
          propLen are integers indicating how wide to make the variable
          and proportion intervals (1 unit is one base pair).    
          plot.IC and plot.nucFreq are logicals respectively indicating
          whether the IC content and the nucleotide frequencies are to
          be drawn on the plot.


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

     Fabian Gallusser, fgallusser@berkeley.edu

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

     'writeConFile',

