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haplo.stats (version 1.7.6)

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

Description

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: haplo.em(), haplo.glm(), haplo.score(), and haplo.power(); all of which have detailed examples in the vignette.

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Version

Install

install.packages('haplo.stats')

Monthly Downloads

2,490

Version

1.7.6

License

GPL (>= 2)

Maintainer

Jason Sinnwell

Last Published

February 23rd, 2016

Functions in haplo.stats (1.7.6)

summary.haplo.glm

Print and summary of a haplo.glm object

Find Location from Mouse Clicks and Print Haplotypes on Plot

geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes

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

Integer Rank Codes for Haplotypes

haplo.score.merge

Merge haplo.score And haplo.group Objects

summary.haplo.em

Summarize contents of a haplo.em object

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 contents of a haplo.em object

Power and sample size for the chi-square distribution

score.sim.control

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

print.haplo.score

Print a haplo.score object

variance-covariance matrix of a fitted haplo.glm object

Set of haplotypes and frequencies for power and sample size calculations

GLM Regression of Trait on Ambiguous Haplotypes

print.haplo.score.slide

Print the contents of a haplo.score.slide object

Frequencies for Haplotypes by Grouping Variable

Power and sample size for the F distribution

haplo.em.control

Create the Control Parameters for the EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci

Haplotype Association Analysis in a Case-Control design

Plot a seqhap object

haplo.score.slide

Score Statistics for Association of Traits with Haplotypes

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

Summarize Full Haplotype Enumeration on Genotype Matrix

haplo.glm.control

Create list of control parameters for haplo.glm

print.haplo.group

Print a haplo.group object

fitted.haplo.glm

Fitted values from haplo.glm fit

haplo.em.fitter

Compute engine for haplotype EM algorithm

Print a haplo.cc object

residuals.haplo.glm

Accessing residuals for haplo.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.

Sequential Haplotype Scan Association Analysis for Case-Control Data

EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci

print.haplo.score.merge

Print a haplo.score.merge object

convert genotype matrix from 1-column 2-column

plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics

Creates an object of class "locus"

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

find.haplo.beta.qt

Find beta coefficients for risk haplotypes, for specified r2

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

Build a design matrix for haplotypes

Simulated data for seqhap examples

print.haplo.scan

Print a haplo.scan object

Get a list of objects for haplotype pairs

consistency checks for x.linked locus

Compute Generalized Inverse of Input Matrix

HLA Loci and Serologic Response to Measles Vaccination

plot.haplo.score.slide

Plot a haplo.score.slide Object

Score Statistics for Association of Traits with Haplotypes

Louis Information for haplo.glm

anova.haplo.glm

Analysis of variance for haplo.glm model fit

haplo.model.frame

Sets up a model frame for haplo.glm

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