AlignedRead            package:ShortRead            R Documentation

_C_o_n_s_t_r_u_c_t _o_b_j_e_c_t_s _o_f _c_l_a_s_s "_A_l_i_g_n_e_d_R_e_a_d"

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

     This function constructs objects of 'AlignedRead'. It will often
     be more convenient to create 'AlignedRead' objects using parsers
     such as 'readAligned'.

_U_s_a_g_e:

     AlignedRead(sread, id, quality, chromosome, position, strand,
                 alignQuality,
                 alignData = AlignedDataFrame(nrow = length(sread)))

_A_r_g_u_m_e_n_t_s:

   sread: An object of class 'DNAStringSet', containing the DNA
          sequences of the short reads.

      id: An object of class 'BStringSet', containing the identifiers
          of the short reads. This object is the same length as
          'sread'.

 quality: An object of class 'BStringSet', containing the ASCII-encoded
          quality scores of the short reads. This object is the same
          length as 'sread'.

chromosome: A 'factor' describing the particular sequence within a set
          of target sequences (e.g. chromosomes in a genome assembly)
          to which each short read aligns.

position: A 'integer' vector describing the (base pair) position at
          which each short read begins its alignment.

  strand: A 'factor' describing the strand to which the short read
          aligns.

alignQuality: A 'numeric' vector describing the alignment quality.

alignData: An 'AlignedDataFrame' with number of rows equal to the
          length of 'sread', containing additional information about
          alignments.

_V_a_l_u_e:

     An object of class 'AlignedRead'.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'AlignedRead'.

