RNAString-class          package:Biostrings          R Documentation

_T_h_e _R_N_A_S_t_r_i_n_g _c_l_a_s_s

_D_e_s_c_r_i_p_t_i_o_n:

     A 'RNAString' object allows efficient storage and manipulation of
     a long RNA sequence.

_D_e_t_a_i_l_s:

     The 'RNAString' class derives directly from the 'BString' class
     (with no additional slot). All functions and methods described in
     the 'BString' man page also work with a 'RNAString' object
     (inheritance).

     Unlike a 'BString' object that allows storage of any non-empty
     string (based on a single-byte character set) a 'RNAString' object
     can only store a non-empty string based on the RNAString alphabet
     (see below). In addition, the letters stored in a 'RNAString'
     object are encoded in a way that optimizes fast search algorithms.

_T_h_e _R_N_A_S_t_r_i_n_g _a_l_p_h_a_b_e_t:

     This alphabet contains all letters from the IUPAC Extended Genetic
     Alphabet (see 'IUPAC_CODE_MAP') where '"T"' is replaced by '"U"' +
     the gap letter '"-"'. It is stored in the 'RNA_ALPHABET' constant
     (character vector). The 'alphabet' method also returns
     'RNA_ALPHABET' when applied to a 'RNAString' object and is
     provided for convenience only.

_C_o_n_s_t_r_u_c_t_o_r-_l_i_k_e _f_u_n_c_t_i_o_n_s _a_n_d _g_e_n_e_r_i_c_s:

     In the code snippet below, 'src' can be a character vector or a
     'BString' (or derived) object.

      'RNAString(src)': [TODO: Document me]

_A_u_t_h_o_r(_s):

     H. Pages

_S_e_e _A_l_s_o:

     'BString', 'IUPAC_CODE_MAP', 'DNAString', 'BStringViews'

_E_x_a_m_p_l_e_s:

       d <- DNAString("TTGAAAA-CTC-N")
       r <- RNAString(d)
       alphabet(r)
       RNA_ALPHABET