Sequence-class            package:IRanges            R Documentation

_S_e_q_u_e_n_c_e _o_b_j_e_c_t_s

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

     The Sequence virtual class is a general container for storing a
     sequence i.e. an ordered set of elements. These containers come in
     two types:  XSequence and XRle.

     The XSequence virtual class is a general container for storing an
     "external sequence". The following classes derive directly from
     the XSequence class.

     The XRaw class is a container for storing an external sequence of
     bytes (stored as char values at the C level).

     The XInteger class is a container for storing an external sequence
     of integer values (stored as int values at the C level).

     The XNumeric class is a container for storing an external sequence
     of numeric values (stored as double values at the C level).

     Also the XString class from the Biostrings package

     The XRle virtual class is a general container for storing an
     "external sequence" that is stored in a run-time encoding format.
     The following classes derive directly from the XRle class.

     The XRleInteger class is a container for storing an external
     run-length encoding of integers (stored as char values at the C
     level).

     The purpose of these containers is to provide a "pass by address"
     semantic and also to avoid the overhead of copying the sequence
     data when a linear subsequence needs to be extracted.

_S_u_b_s_e_t_t_i_n_g:

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


      'subseq(x, start=NA, end=NA, width=NA)': Extract the subsequence
          from 'x' specified by 'start', 'end' and 'width'. The
          supplied start/end/width values are solved by a call to
          'solveUserSEW(length(x), start=start, end=end, width=width)'
          and therefore must be compliant with the rules of the SEW
          (Start/End/Width) interface (see '?solveUserSEW' for the
          details).

          A note about performance: 'subseq' does NOT copy the sequence
          data of an XSequence object. Hence it's very efficient and is
          therefore the recommended way to extract a linear subsequence
          (i.e. a set of consecutive elements) from an XSequence
          object. For example, extracting a 100Mb subsequence from
          Human chromosome 1 (a 250Mb DNAString object) with 'subseq'
          is (almost) instantaneous and has (almost) no memory
          footprint (the cost in time and memory does not depend on the
          length of the original sequence or on the length of the
          subsequence to extract).

      'x[i, drop=TRUE]': Return a new Sequence object made of the
          selected elements (subscript 'i' must be an NA-free numeric
          vector specifying the positions of the elements to select).
          The 'drop' argument specifies whether or not to coerce the
          returned sequence to a standard vector.

      'rep(x, times)': Return a new Sequence object made of the
          repeated elements.


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

     Views-class, 'solveUserSEW', DNAString-class

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

       x1 <- XInteger(12, c(-1:10))
       x1
       length(x1)

       ## Subsetting
       x2 <- XInteger(99999, sample(99, 99999, replace=TRUE) - 50)
       x2
       subseq(x2, start=10)
       subseq(x2, start=-10)
       subseq(x2, start=-20, end=-10)
       subseq(x2, start=10, width=5)
       subseq(x2, end=10, width=5)
       subseq(x2, end=10, width=0)

       x1[length(x1):1]
       x1[length(x1):1, drop=FALSE]

