maxchi: Stepwise detection of recombination breakpoints using MaxChi
In stepwise: Stepwise detection of recombination breakpoints

Description Usage Arguments Details Value Author(s) References See Also Examples

Stepwise detection of recombination breakpoints using the maximum chi-square (MaxChi) method at each step

1	maxchi(input_file, breaks, winHalfWidth, permReps)

`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

The maxchi function implements the maximum chi-square (MaxChi) method for detecting recombination breakpoints (Maynard Smith 1992) 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 pair of sequences, a chi-square statistic is computed to compare two proportions: the proportion of sites at which the sequences agree in the left half-window and the proportion of sites in at which the sequences agree in the right half-window. Discordance between the two proportions may reflect a recombination event, located at the window centre, in the history of the two sequences. The maximum chi-square over all sequence pairs is regarded as a summary of the evidence for recombination at the window centre. The individual chi-square statistics may also be of interest for suggesting pairs of sequences segments that descend from historical recombination events. Significance of observed chi-square 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).

`polyposn`	The site numbers of all ungapped polymorphic sites in the alignment
`chisqs`	Observed chi-square statistics that exceed the 90th percentile of the permutation null distribution
`winlocs`	Window centres corresponding to the chi-square statistics in `chisqs`
`pairmem1`	First member of each pair that lead to a significant chi-square statistic in `chisqs`
`pairmem2`	Second member of each pair
`quants`	90th and 95th percentiles of the permutation distribution

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

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

Maynard Smith J (1992). Analyzing the mosaic structure of genes. J Mol Evol, 34:126-129.

http://stat-db.stat.sfu.ca/stepwise

summary.maxchi, phylpro