AtoR                  package:GeneR                  R Documentation

_C_o_n_v_e_r_s_i_o_n _o_f _a_d_d_r_e_s_s_e_s

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

     Converts addresses on a sequence according to the working strand 
     and the address type (A : absolute, T : true, R : relative) .

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

     AtoR(x, seqno=0)
     AtoT(x, seqno=0)
     RtoA(x, seqno=0)
     RtoT(x, seqno=0)
     TtoA(x, seqno=0)
     TtoR(x, seqno=0)

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

       x: Integer/vector. Addresses 

   seqno: Integer/scalar, Sequence number (buffer number)

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

     All details on addresses and global variables are on the page
     'globals'.

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

     Integer vector with new addresses

_N_o_t_e:

     All results depend on the value of Strand. See: 'setStrand',
     'getStrand'.

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

     L. Cottret

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

     'AtoT', 'RtoA', 'RtoT', 'TtoA', 'TtoR','setStrand', 'getStrand'

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

     s<-"cgtagtagctagctagctagctagctagc"
     placeString (s, seqno=0)
     # s of size 30
     address <- c(4,20)

     # On reverse strand:
     setStrand(1)
     AtoR(address)
     #[1] 26 10

     # On forward strand does nothing:
     setStrand(0)
     AtoR(address)
     #[1]  4 20

