Statistical Analysis of Haplotypes with Traits and Covariates when Linkage Phase is Ambiguous

---

Documentation for package ‘haplo.stats’ version 1.9.5.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

anova.haplo.glm	Analysis of variance for haplo.glm model fit
anova.haplo.glmlist	Analysis of variance for haplo.glm model fit
chisq.power	Power and sample size for the chi-square distribution
chisq.power.dif	Power and sample size for the chi-square distribution
chisq.sample.size	Power and sample size for the chi-square distribution
dglm.fit	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
f.power	Power and sample size for the F distribution
f.power.dif	Power and sample size for the F distribution
f.sample.size	Power and sample size for the F distribution
find.beta.qt.phase.known	Find beta coefficients for risk haplotypes, for specified r2
find.haplo.beta.qt	Find beta coefficients for risk haplotypes, for specified r2
find.intercept.logistic	Compute either power or sample size for haplotype associations in a case-control study.
find.intercept.qt.phase.known	Find beta coefficients for risk haplotypes, for specified r2
fitted.haplo.glm	Fitted values from haplo.glm fit
geno.count.pairs	Counts of Total Haplotype Pairs Produced by Genotypes
geno1to2	convert genotype matrix from 1-column 2-column
get.hapPair	Get a list of objects for haplotype pairs
Ginv	Compute Generalized Inverse of Input Matrix
haplo.binomial	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
haplo.cc	Haplotype Association Analysis in a Case-Control design
haplo.chistat	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
haplo.design	Build a design matrix for haplotypes
haplo.em	EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em.control	Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.em.fitter	Compute engine for haplotype EM algorithm
haplo.enum	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
haplo.glm	GLM Regression of Trait on Ambiguous Haplotypes
haplo.glm.control	Create list of control parameters for haplo.glm
haplo.group	Frequencies for Haplotypes by Grouping Variable
haplo.hash	Integer Rank Codes for Haplotypes
haplo.model.frame	Sets up a model frame for haplo.glm
haplo.power.cc	Compute either power or sample size for haplotype associations in a case-control study.
haplo.power.cc.ncp	Compute either power or sample size for haplotype associations in a case-control study.
haplo.power.qt	Compute either power or sample size for haplotype associations with a quantitative trait.
haplo.power.qt.ncp	Compute either power or sample size for haplotype associations with a quantitative trait.
haplo.scan	Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window
haplo.scan.obs	Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window
haplo.scan.sim	Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window
haplo.score	Score Statistics for Association of Traits with Haplotypes
haplo.score.glm	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
haplo.score.merge	Merge haplo.score And haplo.group Objects
haplo.score.podds	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
haplo.score.slide	Score Statistics for Association of Traits with Haplotypes
hapPower.demo	Set of haplotypes and frequencies for power and sample size calculations
hla.demo	HLA Loci and Serologic Response to Measles Vaccination
locator.haplo	Find Location from Mouse Clicks and Print Haplotypes on Plot
locus	Creates an object of class "locus"
louis.info	Louis Information for haplo.glm
mf.gindx	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
na.geno.keep	Remove rows with NA in covariates, but keep genotypes with NAs
plot.haplo.score	Plot Haplotype Frequencies versus Haplotype Score Statistics
plot.haplo.score.slide	Plot a haplo.score.slide Object
plot.seqhap	Plot a seqhap object
print.haplo.cc	Print a haplo.cc object
print.haplo.em	Print contents of a haplo.em object
print.haplo.glm	GLM Regression of Trait on Ambiguous Haplotypes
print.haplo.group	Print a haplo.group object
print.haplo.scan	Print a haplo.scan object
print.haplo.score	Print a haplo.score object
print.haplo.score.merge	Print a haplo.score.merge object
print.haplo.score.slide	Print the contents of a haplo.score.slide object
print.seqhap	Sequential Haplotype Scan Association Analysis for Case-Control Data
print.summary.haplo.glm	Print and summary of a haplo.glm object
printBanner	Print a nice banner
residScaledGlmFit	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
residuals.haplo.glm	Accessing residuals for haplo.glm fit
score.sim.control	Create the list of control parameters for simulations in haplo.score
seqhap	Sequential Haplotype Scan Association Analysis for Case-Control Data
seqhap.dat	Simulated data for seqhap examples
seqhap.pos	Simulated data for seqhap examples
setupGeno	Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.
sr.class	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
sr.class<-	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
summary.haplo.em	Summarize contents of a haplo.em object
summary.haplo.glm	Print and summary of a haplo.glm object
summaryGeno	Summarize Full Haplotype Enumeration on Genotype Matrix
varfunc.glm.fit	Internal functions for the HaploStats package. See the help file for the main functions (haplo.em, haplo.score, haplo.glm) for details on some of these functions.
vcov.haplo.glm	variance-covariance matrix of a fitted haplo.glm object
x.sexcheck	consistency checks for x.linked locus