matchSeeds             package:microRNA             R Documentation

_A _f_u_n_c_t_i_o_n _t_o _m_a_t_c_h _s_e_e_d _r_e_g_i_o_n_s _t_o _s_e_q_u_e_n_c_e_s.

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

     Given an input set of seed regions and a set of sequences all
     locations of the seed regions (exact matches) within the sequences
     are found.

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

     matchSeeds(seeds, seqs)

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

   seeds: The seeds, or short sequences, to match. 

    seqs: The sequences to find matches in. 

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

     We presume that the problem is an exact matching problem and that
     all sequences are in the correct orientation for that.  If, for
     example, you start with seed regions from a microRNA (for 'seeds')
     and 3'UTR sequences (for 'seqs'), then you would want to reverse
     complement one of the two sequences. And make sure all sequences
     are either DNA or RNA.

     Names from either 'seeds' or 'seqs' are propogated, as much as is
     possible.

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

     A list containing one entry for each element of 'seeds' that had
     at least one match in one entry of 'seqs'. Each element of this
     list is a named vector containing the elements of 'seqs' that the
     corresponding seed has an exact match in.

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

     R. Gentleman

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

     'seedRegions'

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

     data(hsSeqs)
     data(s3utr)
     hSeedReg = seedRegions(hsSeqs)
     comphSeed = revcompRNA(hSeedReg)
     comph = RNA2DNA(comphSeed)
     names(comph) = names(hsSeqs)
     mx = matchSeeds(comph, s3utr)

