seedRegions             package:microRNA             R Documentation

_A _f_u_n_c_t_i_o_n _t_o _r_e_t_r_i_e_v_e _t_h_e _s_e_e_d _r_e_g_i_o_n_s _f_r_o_m _m_i_c_r_o_R_N_A _s_e_q_u_e_n_c_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     The seed region of a microRNA consists of a set of nucleotides at
     the 5' end of the microRNA, typically bases 2 through 7, although
     some times 8 is used.

_U_s_a_g_e:

     seedRegions(x, start = 2, stop = 7)

_A_r_g_u_m_e_n_t_s:

       x: A vector of microRNA sequences. 

   start: The start locations, can be a vector. 

    stop: The stop locations, can be a vector. 

_D_e_t_a_i_l_s:

     We use 'substr' to extract these sequences.

_V_a_l_u_e:

     A vector of the same length as 'x' with the substrings.

_A_u_t_h_o_r(_s):

     R. Gentleman

_S_e_e _A_l_s_o:

     'substr'

_E_x_a_m_p_l_e_s:

      data(hsSeqs)
      seedRegions(hsSeqs[1:5])
      seedRegions(hsSeqs[1:3], start=c(2,1,2), stop=c(8,7,9))

