ShortRead-class          package:ShortRead          R Documentation

"_S_h_o_r_t_R_e_a_d" _c_l_a_s_s _f_o_r _s_h_o_r_t _r_e_a_d_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, uniform-length short reads and their
     identifiers.

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

     Objects from this class are not normally created directly by the
     user.

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


     '_s_r_e_a_d': Object of class '"DNAStringSet"' containing
          IUPAC-standard, uniform-length DNA strings represent short
          sequence reads.

     '_i_d': Object of class '"BStringSet"' containing identifiers, one
          for each short read.

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

     Class '".ShortReadBase"', directly.

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

     See 'accessors' for slot accessor functions.


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

     _l_e_n_g_t_h 'signature(x = "ShortRead")': returns a 'integer(1)' vector
          describing the number of reads in this object.

     _w_i_d_t_h 'signature(x = "ShortRead")': returns a 'integer(1)' vector
          describing the number of characters in each read in this
          object.

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

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

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

     _s_r_d_u_p_l_i_c_a_t_e_d '\signature{x = "ShortRead"}': Order, rank, sort, and
          find duplicates in 'ShortRead' objects based on 'sread(x)',
          analogous to the corresponding functions 'order', 'rank',
          'sort', and 'duplicated', ordering nucleotides in the order
          'ACGT'.

     _s_r_d_i_s_t_a_n_c_e '\signature{pattern="ShortRead", subject="ANY"}': Find
          the edit distance between each read in 'pattern' and the
          (short) sequences in 'subject'. See 'srdistance' for
          allowable values for 'subject', and for additional details.

     _a_l_p_h_a_b_e_t_B_y_C_y_c_l_e 'signature(stringSet = "ShortRead")': Apply
          'alphabetByCycle' to the 'sread' component of 'stringSet',
          returning a matrix as described in 'alphabetByCycle'.

     _t_a_b_l_e_s 'signature(x= "ShortRead", n = 50)': Apply 'tables' to the
          'sread' component of 'x', returning a list summarizing
          frequency of reads in 'x'.

     _c_l_e_a_n 'signature(object="ShortRead")': Remove all reads containing
          non-nucleotide ('"N", "-"') symbols.

     _s_h_o_w 'signature(object = "ShortRead")': provides a brief summary
          of the object, including its class, length and width.

     _d_e_t_a_i_l 'signature(object = "ShortRead")': provides a more
          extensive summary of this object, displaying the first and
          last entries of 'sread' and 'id'.

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

     Martin Morgan

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

     'ShortReadQ'

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

     showClass("ShortRead")
     showMethods(class="ShortRead")

