ShortReadQ-class          package:ShortRead          R Documentation

"_S_h_o_r_t_R_e_a_d_Q" _c_l_a_s_s _f_o_r _s_h_o_r_t _r_e_a_d_s _a_n_d _t_h_e_i_r _q_u_a_l_i_t_y _s_c_o_r_e_s

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

     This class provides a way to store and manipulate, in a
     coordinated fashion, the reads, identifiers, and quality scores of
     uniform-length short reads.

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

     Objects from this class are the result of 'readFastq', or can be
     constructed from 'DNAStringSet', 'QualityScore', and 'BStringSet'
     objects, as described below.

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

     Slots 'sread' and 'id' are inherited from 'ShortRead'. An
     additional slot defined in this class is:

     '_q_u_a_l_i_t_y': Object of class '"BStringSet"' representing a quality
          score (see 'readFastq' for some discussion of quality score).

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

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

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

     Constructors include:



     _S_h_o_r_t_R_e_a_d_Q 'signature(sread = "DNAStringSet", quality =
          "QualityScore", id = "BStringSet")': Create a 'ShortReadQ'
          object from reads, their quality scores, and identifiers. The
          length of 'id' and 'quality'must match that of 'sread'.

     _S_h_o_r_t_R_e_a_d_Q 'signature(sread = "DNAStringSet", quality =
          "QualityScore", id = "missing")': Create a 'ShortReadQ'
          object from reads and their quality scores, creating empty
          identifiers.

     _S_h_o_r_t_R_e_a_d_Q 'signature(sread = "missing", quality = "missing", id =
          "missing", ...)': Create an empty 'ShortReadQ' object.


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



     _w_r_i_t_e_F_a_s_t_q 'signature(object = "ShortReadQ", file = "character",
          mode="character", ...)': Write 'object' to 'file' in fastq
          format. 'mode' defaults to w. This creates a new file, or
          fails if 'file' already exists. Use 'mode="a"' to append to
          an existing file. 'file' is expanded using 'path.expand'.

     [ 'signature(x = "ShortReadQ", i = "ANY", j = "missing")':  This
          method creates a new 'ShortReadQ' object containing only
          those reads indexed by 'i'. Additional methods on
          [,ShortRead do not provide additional functionality, but
          are present to limit inappropriate use.

     _a_p_p_e_n_d 'signature(x = "ShortReadQ", values = "ShortRead", length =
          "missing")': append the 'sread', 'quality' and 'id' slots of
          'values' after the corresponding fields of 'x'.

     _n_a_r_r_o_w 'signature(x = "ShortReadQ", start = NA, end = NA, width =
          NA, use.names = TRUE)': narrow 'sread' and 'qualilty' so
          that sequences are between 'start' and 'end' bases, according
          to 'narrow' in the 'IRanges' package.

     _a_l_p_h_a_b_e_t_B_y_C_y_c_l_e 'signature(stringSet = "ShortReadQ")': Apply
          'alphabetByCycle' to the 'sread' component, the 'quality'
          component, and the combination of these two components of
          'stringSet', returning a list of matrices with three
          elements: '"sread"', '"quality"', and '"both"'.

     _a_l_p_h_a_b_e_t_S_c_o_r_e 'signature(object = "ShortReadQ")': See
          'alphabetScore' for details.

     _d_e_t_a_i_l 'signature(object = "ShortReadQ")': display the first and
          last entries of each of 'sread', 'id', and 'quality' entries
          of 'object'.

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

     Martin Morgan

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

     'readFastq' for creation of objects of this class from
     fastq-format files.

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

     showClass("ShortReadQ")
     showMethods(class="ShortReadQ", inherit=FALSE)
     showMethods(class="ShortRead", inherit=FALSE)

