phylpro               package:stepwise               R Documentation

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

     Stepwise detection of recombination breakpoints using phylogenetic
     profiling (Phylpro) at each step

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

      phylpro(input_file, breaks, winHalfWidth, permReps) 

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

input_file: character string indicating the name of a Phylip format
          data input file

  breaks: an integer vector of ordered site(s) just before the
          previously declared breakpoints

winHalfWidth: the window half width to use

permReps: the number of Monte Carlo replicates to use for the
          permutation distribution

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

     The phylpro function implements phylogenetic profiling (Phylpro)
     for detecting recombination breakpoints (Weiller 1998) using a
     moving window of fixed width. Breakpoints detected in previous
     steps of a stepwise search may be conditioned upon.

     For a given position of the moving window on the sequence
     alignment, and for a given "target" sequence, a correlation is
     computed to compare two distance vectors: the distance between the
     target sequence and all other sequences in the left half-window
     and the distance between the target sequence and all others in the
     right half-window. The pair-wise distance measure used is the
     proportion of sites at which the sequences differ. Discordance
     between the two distance vectors may reflect a recombination
     event, located at the window centre, in the history of the target
     sequence. The minimum correlation over all target sequences is
     regarded as a summary of the evidence for recombination at the
     window centre. The individual correlations for the target
     sequences may also be of interest for suggesting sequence segments
     that descend from historical recombination events. Significance of
     observed correlation statistics is assessed by a Monte Carlo
     permutation test. When conditioning on breakpoints proposed at
     previous steps of a stepwise search, permutation is restricted to
     sites within blocks defined by the previously proposed
     breakpoints, as described by Graham et al. (2004).

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

polyposn: The site numbers of all ungapped polymorphic sites in the
          alignment

   corrs: Observed correlations that exceed the 90th percentile of the
          permutation null distribution

 winlocs: Window centres corresponding to the correlations in 'corrs'

target.seqs: The target sequence that lead to a significant correlation
          in 'corrs'

  quants: 90th and 95th percentiles of the permutation distribution

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

     Brad McNeney <mcneney@stat.sfu.ca>, Jinko Graham
     <jgraham@stat.sfu.ca>, Sigal Blay <sblay@sfu.ca>

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

     Graham J, McNeney B and Seillier-Moiseiwitsch F (2004). Stepwise
     detection of recombination breakpoints in sequence alignments.
     _Bioinformatics_ Sep 23; [Epub ahead of print]

     Weiller G (1998). Phylogenetic profiles: A graphical method for
     detecting genetic recombination in homologous sequences. _Mol Biol
     Evol_, *15*:326-335.

     <URL: http://stat-db.stat.sfu.ca/stepwise>

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

     'summary.phylpro', 'maxchi'

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

      demo(phylpro) 

