MaskedXString-class        package:Biostrings        R Documentation

_M_a_s_k_e_d_X_S_t_r_i_n_g _o_b_j_e_c_t_s

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

     The MaskedXString class is a container for storing a masked
     sequence.

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

     [TODO]

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

     In the code snippets below, 'x' is a MaskedXString object.


      'unmasked(x)': Turns 'x' into an XString object by dropping the
          masks.

      'masks(x)': Turns 'x' into a MaskCollection object by dropping
          the sequence.

      'alphabet(x)': Equivalent to 'alphabet(unmasked(x))'. See
          '?alphabet' for more information.

      'length(x)': Equivalent to 'length(unmasked(x))'. See
          '?`length,XString-method`' for more information.


"_m_a_s_k_e_d_w_i_d_t_h" _a_n_d _r_e_l_a_t_e_d _m_e_t_h_o_d_s:

     In the code snippets below, 'x' is a MaskedXString object.


      'maskedwidth(x)': Get the number of masked letters in 'x'. A
          letter is considered masked iff it's masked by at least one
          active mask.

      'maskedratio(x)': Equivalent to 'maskedwidth(x) / length(x)'.

      'nchar(x)': Equivalent to 'length(x) - maskedwidth(x)'.


_C_o_e_r_c_i_o_n:

     TODO

_O_t_h_e_r _m_e_t_h_o_d_s:

     TODO

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

     H. Pages

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

     'maskMotif', 'alphabetFrequency', 'reverse', XString-class,
     MaskCollection-class, XStringViews-class, IRanges-utils

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

       ## Masking by position
       mask0 <- Mask(mask.width=29, start=c(3, 10, 25), width=c(6, 8, 5))
       x <- DNAString("ACACAACTAGATAGNACTNNGAGAGACGC")
       masks(x) <- mask0
       x
       gaps(x)

       ## See ?maskMotif for masking by content

