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Method to plot an object of class seqhap. The p-values at each locus are based on sequentially combined loci, and they are plotted to visualize the p-values when scanning each locus using seqhap methods. Plots -log10(p-value) on the y-axis vs. the loci over which it was computed on the x-axis.
● Data Source:
CranContrib
● Keywords:
● Alias: plot.seqhap
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Much like the R/Splus locator function is used to find x-y coordinates on a plot. Find all x-y coordinates that are chosen by the user's mouse clicks. Then print haplotype labels at the chosen positions.
● Data Source:
CranContrib
● Keywords:
● Alias: locator.haplo
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Search for haplotypes that have the strongest association with a binary trait (typically case/control status) by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window. For each haplotype length, a score statistic is computed to compare the set of haplotypes with a given length between cases versus controls. The locus-specific score statistic is the maximum score statistic calculated on loci containing that locus. The maximum score statistic over all haplotype lengths within all possible windows is used for a global test for association. Permutations of the trait are used to compute p-values.
● Data Source:
CranContrib
● Keywords:
● Alias: haplo.scan, haplo.scan.obs, haplo.scan.sim
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Power and sample size for the F distribution given non-centrality, degrees of freedom, alpha, N (for f.power), and power (for f.sample.size)
● Data Source:
CranContrib
● Keywords: power
● Alias: f.power, f.power.dif, f.sample.size
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vcov.haplo.glm
(Package: haplo.stats) :
variance-covariance matrix of a fitted haplo.glm object
Returns the variance-covariance matrix of the main parameters of a fitted haplo.glm object
● Data Source:
CranContrib
● Keywords: glm
● Alias: vcov.haplo.glm
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Find betas for risk haplotypes and intercept (beta for base.index haplotype) with a given r2
● Data Source:
CranContrib
● Keywords: power
● Alias: find.beta.qt.phase.known, find.haplo.beta.qt, find.intercept.qt.phase.known
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Power and sample size for the chi-square distribution given non-centrality, degrees of freedom, alpha, N (for chisq.power), and power (for chisq.sample.size)
● Data Source:
CranContrib
● Keywords: power
● Alias: chisq.power, chisq.power.dif, chisq.sample.size
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The fitted values for each person, collapsed over their expanded fitted values due to their multiple possible haplotype pairs
● Data Source:
CranContrib
● Keywords: glm
● Alias: fitted.haplo.glm
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Do print and summary as in regular glm, then display extra information on haplotypes used in the model fit
● Data Source:
CranContrib
● Keywords: glm
● Alias: print.summary.haplo.glm, summary.haplo.glm
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Print the data frame returned from haplo.score.slide
● Data Source:
CranContrib
● Keywords:
● Alias: print.haplo.score.slide
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providing 
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