makeConSet               package:cosmo               R Documentation

_C_o_n_s_t_r_u_c_t_i_n_g _a _c_o_n_s_t_r_a_i_n_t _s_e_t.

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

     The first step to building a constraint set is to define the
     number and type of intervals defining the set. This is done using
     the makeConSet function.  Constraints are then built using the
     makeBoundCon (for information content bounding constraints),
     makeIntFreqCon (for interval nucleotide frequency constraints),
     makePosFreqCon (for position frequency constraints) and finally
     makeShapeCon (for shape constraints). The constraints are then
     added to the sets created with makeConSet using the addCon
     command.

_U_s_a_g_e:

     makeConSet(numInt,type,length,descrip="Constraint Set")

_A_r_g_u_m_e_n_t_s:

  numInt: integer relating to the number of intervals composing the set

    type: character vector describing the types of each of the
          intervals composing the set: the length of this vector should
          be equal to the 'numInt' argument. Possible values are 'B'
          for basepairs, 'V' for variable, and 'P' for proportion

  length: numeric vector of length 'numInt', with a numeric argument
          describing the lengths of the intervals: either the number of
          basepairs if type is 'B',  proportion coefficent if type is
          'P'. For type 'V', the value is of no importance.

 descrip: a character string to describe the constraint set.

_D_e_t_a_i_l_s:

     These commands are an alternative to the GUI for constucting
     constraint sets and groups.

_V_a_l_u_e:

     Null. Depending on the arguments, 1, 2 or 3 text files are
     created, by default in the working directory.

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

     Fabian Gallusser, fgallusser@berkeley.edu

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

     'boundCon', 'subMotifCon', 'posFreqCon', 'shapeCon',
     'shapeDiffCon', 'palCon'

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

     makeConSet(4,c("B","P","V","B"),c(4,50,NA,3))

