AlignedRead-class         package:ShortRead         R Documentation

"_A_l_i_g_n_e_d_R_e_a_d" _c_l_a_s_s _f_o_r _a_l_i_g_n_e_d _s_h_o_r_t _r_e_a_d_s

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

     This class represents and manipulates reads and their genomic
     alignments. Alignment information includes genomic position,
     strand, quality, and other data.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects of this class can be created from a call to the
     'AlignedRead' constructor, or more typically by parsing
     appropriate files (e.g., 'readAligned').

_S_l_o_t_s:



     '_c_h_r_o_m_o_s_o_m_e': Object of class '"factor"' the particular sequence
          within a set of target sequences (e.g. chromosomes in a
          genome assembly) to which each short read aligns.

     '_p_o_s_i_t_i_o_n': Object of class '"integer"' the (base-pair) position
          in the genome to which the read is aligned.

     '_s_t_r_a_n_d': Object of class '"factor"' the strand of the alignment.

     '_a_l_i_g_n_Q_u_a_l_i_t_y': Object of class '"numeric"' representing an
          alignment quality score.

     '_a_l_i_g_n_D_a_t_a': Object of class '"AlignedDataFrame"' additional
          alignment information.

     '_q_u_a_l_i_t_y': Object of class '"BStringSet"' representing base-call
          read quality scores.

     '_s_r_e_a_d': Object of class '"DNAStringSet"' DNA sequence of the
          read.

     '_i_d': Object of class '"BStringSet"' read identifier.


_E_x_t_e_n_d_s:

     Class '"ShortReadQ"', directly. Class '"ShortRead"', by class
     "ShortReadQ", distance 2. Class '".ShortReadBase"', by class
     "ShortReadQ", distance 3.

_M_e_t_h_o_d_s:

     See 'accessors' for additional functions to access slot content,
     and 'ShortReadQ', 'ShortRead' for inherited methods. Additional
     methods include:



     [ 'signature(x = "AlignedRead", i = "ANY", j = "missing")':  This
          method creates a new 'AlignedRead' object containing only
          those reads indexed by 'i'. 'chromosome' is recoded to
          contain only those levels in the new subset.

     _s_t_r_a_n_d 'signature(object = "AlignedRead")': access the strand slot
          of 'object'.

     _c_o_v_e_r_a_g_e 'signature(x = "AlignedRead", start = NA, end = NA, ...,
          coords=c("leftmost", "fiveprime"), extend=0L)':

          Calculate coverage across reads present in 'x'. 

          'start' and 'end' are are regions (e.g., of chromosomes) over
          which coverage is to be calculated. If provided, these are
          length 1 integers or _named_ integer vectors of length
          greater than 1. If named integer vectors, the names must
          match 'levels(chromosome(x))'. If omitted, coverage is
          calculated over the range of values spanned by the reads in
          'x'

          'coords' specifies the coordinate system used to record
          position. Both systems number base pairs from left to right
          on the 5' strand. 'leftmost' indicates the eland convention,
          where 'position(x)' is the left-most (minimum) base pair,
          regardless of strand. 'fiveprime' is the MAQ convetion, where
          'position(x)' is the coordinate of the 5' end of the aligned
          read.

          'extend' indicates the number of base pairs to extend the
          read. Extension is in the 3' direction, measured from the 3'
          end of the aligned read.


     _s_r_o_r_d_e_r '\signature{x = "AlignedRead"}':

     _s_r_r_a_n_k '\signature{x = "AlignedRead"}':

     _s_r_s_o_r_t '\signature{x = "AlignedRead"}':

     _s_r_d_u_p_l_i_c_a_t_e_d '\signature{x = "AlignedRead"}': Order, rank, sort,
          and find duplicates in 'AlignedRead' objects. Reads are
          sorted by 'chromosome', 'strand', 'position', and then
          'sread'; less fine-grained sorting can be accomplished with,
          e.g., 'x[srorder(sread(x))]'.

     _s_h_o_w 'signature(object = "AlignedRead")': provide a compact
          display of the 'AlignedRead'  content.

     _d_e_t_a_i_l 'signature(object = "AlignedRead")': display 'alignData' in
          more detail.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     'readAligned'

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

     showMethods(class="AlignedRead")
     dirPath <- system.file('extdata', 'maq', package='ShortRead')
     readAligned(dirPath, 'out.aln.1.txt', type="MAQMapview")

