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

## Documentation for package ‘haplo.stats’ version 1.6.3

- 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