dustyScore             package:ShortRead             R Documentation

_S_u_m_m_a_r_i_z_e _l_o_w-_c_o_m_p_l_e_x_i_t_y _s_e_q_u_e_n_c_e_s

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

     'dustyScore' identifies low-complexity sequences, in a manner
     inspired by the 'dust' implementation in 'BLAST'.

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

     dustyScore(x, ...)

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

       x: A 'DNAStringSet' object, or object derived from 'ShortRead',
          containing a collection of reads to be summarized.

     ...: Additional arguments, not currently used.

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

     The following methods are defined:


     _d_u_s_t_y_S_c_o_r_e 'signature(x = "DNAStringSet")': operating on an object
          derived from class 'DNAStringSet'.

     _d_u_s_t_y_S_c_o_r_e 'signature(x = "ShortRead")': operating on the 'sread'
          of an object derived from class 'ShortRead'.


     The dust-like calculations used here are as implemented at <URL:
     https://stat.ethz.ch/pipermail/bioc-sig-sequencing/2009-February/000170.html>.
     Scores range from 0 (all triplets unique) to the square of the
     width of the longest sequence (poly-A, -C, -G, or -T).

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

     A vector of numeric scores, with length equal to the length of
     'x'.

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

     Herve Pages (code); Martin Morgan

_R_e_f_e_r_e_n_c_e_s:

     Morgulis, Getz, Schaffer and Agarwala, 2006. WindowMasker:
     window-based masker for sequenced genomes, Bioinformatics 22:
     134-141.

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

     The WindowMasker supplement defining 'dust' <URL:
     ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/windowmasker/windowmasker_suppl.pdf>

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

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

