constraintSet-class          package:cosmo          R Documentation

_C_l_a_s_s "_c_o_n_s_t_r_a_i_n_t_S_e_t" ~~~

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

     An object of class '"constraintSet"' regroups all the constraints
     one wishes to impose when performing detection. The object consits
     essentially of constraints on the motif broken down into seperate
     intervals, objects of class '"intInfo"'

_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('constraintSet','
      '    description      = ...., # Object of class
     \code{"character"}'
      '    numIntervals     = ...., # Object of class \code{"numeric"}'
      '    intervals        = ...., # Object of class \code{"list"}'
      '    shapeDiffCon     = ...., # Object of class
     \code{"data.frame"}'
      '    subMotifCon      = ...., # Object of class
     \code{"data.frame"}'
      '    palCon           = ...., # Object of class
     \code{"data.frame"}'
      '    objectCall       = ...., # Object of class \code{"call"}'
      '  )'

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


     '_d_e_s_c_r_i_p_t_i_o_n': Object of class '"character"' a general description
          of the constraint set 

     '_n_u_m_I_n_t_e_r_v_a_l_s': Object of class '"numeric"' number of intervals
          the motif was split into 

     '_i_n_t_e_r_v_a_l_s': Object of class '"list"' a list of objects of class
          '"intInfo"' each describing the constraints imposed on the
          individual intervals    

     '_s_h_a_p_e_D_i_f_f_C_o_n': Object of class '"data.frame"' a data frame
          summarizing the global constraints of the shape constraints.
          The data frame has four columns: the first two columns are
          the intervals and the extremity subject to the constraint,
          the extremity being supplied as 'a' for beginning, and 'b'
          for end. The third and fourth column are respectively the
          lower and upper bounds on the difference between the interval
          extremities considered. For example, if c("1b","2a",-0.2,0.5)
          were a row in the data frame, it would indicate that the
          difference in the information content between the end of the
          first interval and the beginning of the second should be
          between -0.2 and 0.5.    

     '_s_u_b_M_o_t_i_f_C_o_n': Object of class '"data.frame"' a data frame
          specifying the submotif global constraints. The two columns
          respectiuvely indicate the submotif of interest and it's
          error tolerance. The error is computed as the difference in
          terms       of frequency between the submotif and the
          position weight matrix.    

     '_p_a_l_C_o_n': Object of class '"data.frame"' a data frame summarizing
          the palindromic constraints imposed on the motif: the first
          two columns indicate the two palindromic intervals and the
          third is the error tolerated between the nucleotide
          frequencies in both intervals.     

     '_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 = "constraintSet", varLen=4, propLen=4,
          plot.IC=TRUE, plot.nucFreq=TRUE)': Plots the
          '"constraintSet"' 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.

     _p_r_i_n_t 'signature(x = "constraintSet",...)' Prints the constraint
          set in the standard cosmo format.

     _s_h_o_w 'signature(object = "constraintSet")' Prints the constraint
          set in the standard cosmo format.


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

     Fabian Gallusser, fgallusser@berkeley.edu

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

     'writeConFile',  'constraintSet-class', 'intInfo-class'

