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 created by 'readFasta', or by calls to
     the constructor 'ShortRead', as outlined below.

_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:

     Constructors include:



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

     _S_h_o_r_t_R_e_a_d 'signature(sread = "DNAStringSet", id = "missing")':
          Create a 'ShortRead' object from reads, creating empty
          identifiers.

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


     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.

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

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


     _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 an 'integer()' vector
          of the widths of 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.

     _t_r_i_m_L_R_P_a_t_t_e_r_n_s 'signature(Lpattern = "", Rpattern = "", subject =
          "ShortRead", max.Lmismatch = 0, max.Rmismatch = 0,
          with.Lindels = FALSE, with.Rindels = FALSE, Lfixed = TRUE,
          Rfixed = TRUE, ranges = FALSE)':

          Remove left and / or right flanking patterns from
          'sread(subject)', as described in 'trimLRPatterns'. Classes
          derived from 'ShortRead' (e.g., 'ShortReadQ', 'AlignedRead')
          have corresponding base quality scores trimmed, too. A
          user-supplied argument 'ranges' is ignored by this method;
          the class of the return object is the same as the class of
          'subject'.

     _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")

