DNAString-class          package:Biostrings          R Documentation

_D_N_A_S_t_r_i_n_g _o_b_j_e_c_t_s

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

     A DNAString object allows efficient storage and manipulation of a
     long DNA sequence.

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

     The DNAString class is a direct XString subclass (with no
     additional slot). Therefore all functions and methods described in
     the XString man page also work with a DNAString object
     (inheritance).

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

_T_h_e _D_N_A _a_l_p_h_a_b_e_t:

     This alphabet contains all letters from the IUPAC Extended Genetic
     Alphabet (see '?IUPAC_CODE_MAP') + the gap ('"-"') and the hard
     masking ('"+"') letters. It is stored in the 'DNA_ALPHABET'
     constant (character vector). The 'alphabet' method also returns
     'DNA_ALPHABET' when applied to a DNAString 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, 'x' can be a single string (character
     vector of length 1), a BString object or an RNAString object.


      'DNAString(x="", start=1, nchar=NA)': Tries to convert 'x' into a
          DNAString object by reading 'nchar' letters starting at
          position 'start' in 'x'.


_A_c_c_e_s_s_o_r _m_e_t_h_o_d_s:

     In the code snippet below, 'x' is a DNAString object.


      'alphabet(x, baseOnly=FALSE)': If 'x' is a DNAString object, then
          return the DNA alphabet (see above). See the corresponding
          man pages when 'x' is a BString, RNAString or AAString
          object.


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

     H. Pages

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

     'IUPAC_CODE_MAP', 'letter', XString-class, RNAString-class,
     'reverseComplement', 'alphabetFrequency'

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

       DNA_BASES
       DNA_ALPHABET
       d <- DNAString("TTGAAAA-CTC-N")
       length(d)
       alphabet(d)                 # DNA_ALPHABET
       alphabet(d, baseOnly=TRUE)  # DNA_BASES

