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The `haplo.stats` Package

Overview of haplo.stats

Routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers).

The main functions are described below.

haplo.em

Estimation of haplotype frequencies, and posterior probabilities of haplotype pairs for a subject, conditional on the observed marker data.

haplo.glm

GLM regression models for the regression of a trait on haplotypes, possibly including covariates and interactions. S3 methods for anova and summary have been implemented.

haplo.score

Score statistics to test associations between haplotypes and a wide variety of traits, including binary, ordinal, quantitative, and Poisson.

haplo.design

Uses as input the result from haplo.em(), and makes a design matrix for haplotype dosage, such that modeling haplotypes is similar to how it would be done within haplo.glm(), but without the iteratetively re-weighted least squares steps.

haplo.cc

Runs simple haplo.score and haplo.glm without covariates with combined results for case-control (binomial family) response.

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Version

Install

install.packages('haplo.stats')

Monthly Downloads

1,168

Version

1.9.7

License

GPL (>= 2)

Maintainer

Last Published

September 19th, 2024

Functions in haplo.stats (1.9.7)

geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes

convert genotype matrix from 1-column 2-column

Frequencies for Haplotypes by Grouping Variable

Find Location from Mouse Clicks and Print Haplotypes on Plot

Get a list of objects for haplotype pairs

Set of haplotypes and frequencies for power and sample size calculations

Compute either power or sample size for haplotype associations with a quantitative trait.

Compute either power or sample size for haplotype associations in a case-control study.

Creates an object of class "locus"

plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics

plot.haplo.score.slide

Plot a haplo.score.slide Object

Print contents of a haplo.em object

print.haplo.group

Print a haplo.group object

haplo.em.fitter

Compute engine for haplotype EM algorithm

GLM Regression of Trait on Ambiguous Haplotypes

score.sim.control

Create the list of control parameters for simulations in haplo.score

Build a design matrix for haplotypes

Haplotype Association Analysis in a Case-Control design

Search for a trait-locus by sliding a fixed-width window over each marker locus and scanning all possible haplotype lengths within the window

Print a nice banner

Summarize Full Haplotype Enumeration on Genotype Matrix

HLA Loci and Serologic Response to Measles Vaccination

variance-covariance matrix of a fitted haplo.glm object

residuals.haplo.glm

Accessing residuals for haplo.glm fit

Louis Information for haplo.glm

summary.haplo.em

Summarize contents of a haplo.em object

summary.haplo.glm

Print and summary of a haplo.glm object

Score Statistics for Association of Traits with Haplotypes

Remove rows with NA in covariates, but keep genotypes with NAs

Sequential Haplotype Scan Association Analysis for Case-Control Data

Plot a seqhap object

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

Print a haplo.cc object

Simulated data for seqhap examples

print.haplo.scan

Print a haplo.scan object

Create a group of locus objects from a genotype matrix, assign to 'model.matrix' class.

haplo.score.slide

Score Statistics for Association of Traits with Haplotypes

print.haplo.score.merge

Print a haplo.score.merge object

print.haplo.score

Print a haplo.score object

print.haplo.score.slide

Print the contents of a haplo.score.slide object

consistency checks for x.linked locus

Power and sample size for the F distribution

find.haplo.beta.qt

Find beta coefficients for risk haplotypes, for specified r2

Integer Rank Codes for Haplotypes

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.glm.control

Create list of control parameters for haplo.glm

Compute Generalized Inverse of Input Matrix

Power and sample size for the chi-square distribution

anova.haplo.glm

Analysis of variance for haplo.glm model fit

fitted.haplo.glm

Fitted values from haplo.glm fit

haplo.model.frame

Sets up a model frame for haplo.glm