alphabetByCycle          package:ShortRead          R Documentation

_S_u_m_m_a_r_i_z_e _s_h_o_r_t _r_e_a_d _n_u_c_l_e_o_t_i_d_e _o_r _q_u_a_l_i_t_y _s_c_o_r_e_s _b_y _c_y_c_l_e

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

     'alphabetByCycle' summarizes short read nucleotides or qualities
     by cycle, e.g., returning the number of occurrences of each
     nucleotide 'A, T, G, C' across all reads from 36 cycles of a
     Solexa lane.

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

     alphabetByCycle(stringSet, alphabet, ...)

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

stringSet: A R object representing the collection of reads or quality
          scores to be summarized. All entries in the string set must
          have the same width (i.e., number of characters in each read
          or quality score).

alphabet: The alphabet (character vector of length 1 strings) from
          which the sequences in 'stringSet' are composed. Methods
          often define an appropriate alphabet, so that the user does
          not have to provide one.

     ...: Additional arguments, perhaps used by methods defined on this
          generic.

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

     The default method requires that 'stringSet' extends the
     'XStringSet' class of 'Biostrings'.

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


     _a_l_p_h_a_b_e_t_B_y_C_y_c_l_e 'signature(stringSet = "BStringSet")': this method
          uses an alphabet spanning all ASCII characters, codes
          '1:255'. 


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

     A matrix with number of rows equal to the length of 'alphabet' and
     columns equal to the width of reads or quality scores in the
     string set. Entries in the matrix are the number of times, over
     all reads of the set, that the corresponding letter of the
     alphabet (row) appeared at the specified cycle (column).

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

     Martin Morgan

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

     The IUPAC alphabet in Biostrings.

     <URL: http://www.bioperl.org/wiki/FASTQ_sequence_format> for the
     BioPerl definition of fastq.

     Solexa documentation `Data analysis - documentation : Pipeline
     output and visualisation'.

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

     showMethods("alphabetByCycle")

     sp <- SolexaPath(system.file('extdata', package='ShortRead'))
     rfq <- readFastq(analysisPath(sp), pattern="s_1_sequence.txt")
     alphabetByCycle(sread(rfq))

     abcq <- alphabetByCycle(quality(rfq))
     dim(abcq)
     ## 'high' scores, first and last cycles
     abcq[64:94,c(1:5, 32:36)]

