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 = as.character(reverseComplement(RNAStringSet(hSeedReg)))
     comph = RNA2DNA(comphSeed)
     mx = matchSeeds(comph, s3utr)

