tables               package:ShortRead               R Documentation

_S_u_m_m_a_r_i_z_e _X_S_t_r_i_n_g_S_e_t _r_e_a_d _f_r_e_q_u_e_n_c_i_e_s

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

     This generic summarizes the number of times each sequence occurs
     in an 'XStringSet' instance.

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

     tables(x, n=50, ...)

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

       x: An object for which a 'tables' method is defined.

       n: An 'integer(1)' value determining how many named sequences
          will be present in the 'top' portion of the return value.

     ...: Additional arguments available to methods

_D_e_t_a_i_l_s:

     Methods of this generic summarize the frequency with which each
     read occurs, There are two components to the summary. The reads
     are reported from most common to least common; typically a method
     parameter controls how many reads to report. Methods also return a
     pair of vectors describing how many reads were represented 1, 2,
     ... times. 

     The following methods are defined, in addition to methods
     described in class-specific documentation:


     _t_a_b_l_e_s 'signature(x= "XStringSet", n = 50)': Apply 'tables' to the
          'XStringSet' 'x'.


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

     A list of length two. 

     top: A named integer vector. Names correspond to sequences. Values
          are the number of times the corresponding sequence occurs in
          the 'XStringSet'. The vector is sorted in decreasing order;
          methods typically include a parameter specifying the number
          of sequences to return.

distribution: a 'data.frame' with two columns. 'nOccurrences' is the
          number of times any particular sequence is represented in the
          set (1, 2, ...). 'nReads' is the number of reads with the
          corresponding occurrence.

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

     Martin Morgan <mtmorgan@fhcrc.org>

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

     showMethods("tables")
     sp <- SolexaPath(system.file("extdata", package="ShortRead"))
     aln <- readAligned(sp)
     tables(sread(aln), n=6)
     xyplot(log10(nReads)~log10(nOccurrences),
            tables(sread(aln))$distribution)

