SeqFrag                package:seqinr                R Documentation

_C_l_a_s_s _f_o_r _s_u_b-_s_e_q_u_e_n_c_e_s

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

     'as.SeqFrag' is called by all methods of 'getFrag', but not
     directly by the users. It creates an object sequence of class
     'SeqFrag'.

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

      as.SeqFrag(object, begin, end, compl = FALSE, name = "frag")
      is.SeqFrag(object)

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

  object: an object sequence of class 'seqFastadna', 'seqFastaAA',
          'seqAcnucWeb' or 'seqFrag' 

   begin: the first base of the fragment to get 

     end: the last base of the fragment to get 

   compl: if TRUE, you must give a name for the sequence

    name: the name of the fragment of the sequence 

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

     'as.SeqFrag' returns a biological sequence representing by a
     vector of chars with the following attributes: 

seqMother: the name of the sequence from which the sequence comes

   begin: the position of the first base of the fragment on the mother
          sequence

     end: the position of the last base of the fragment on the mother
          sequence 

   class: 'SeqFrag' which is the newest class of the sequence 

     'is.SeqFrag' returns TRUE if the object is of class Seqfrag.

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

     D. Charif

_R_e_f_e_r_e_n_c_e_s:

      'citation("seqinr")'

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

     'getFrag'

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

      s = read.fasta(File=system.file("sequences/malM.fasta",package = "seqinr"))
      getFrag(s[[1]],1,10)   

