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haplo.stats (version 1.5.5)

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

Description

A suite of R 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, haplo.power, and seqhap. Copyright: 2003 Mayo Foundation for Medical Education and Research.

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Version

Install

install.packages('haplo.stats')

Monthly Downloads

1,656

Version

1.5.5

License

GPL-2 | file LICENSE

Maintainer

Jason Sinnwell

Last Published

February 25th, 2012

Functions in haplo.stats (1.5.5)

Build a design matrix for haplotypes

print.haplo.scan

Print a haplo.scan object

print.haplo.score

Print a haplo.score object

HLA Loci and Serologic Response to Measles Vaccination

convert genotype matrix from 1-column 2-column

Modified from glm.fit function to not warn users for binomial non-integer weights.

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.merge

Merge haplo.score And haplo.group Objects

fitted.haplo.glm

Fitted values from haplo.glm fit

Integer Rank Codes for Haplotypes

Print contents of a haplo.em object

haplo.em.fitter

Compute engine for haplotype EM algorithm

haplo.glm.control

Create list of control parameters for haplo.glm

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

Get a list of objects for haplotype pairs

Print a haplo.cc object

summary.haplo.glm

Print and summary of a haplo.glm object

haplo.score.slide

Score Statistics for Association of Traits with Haplotypes

Summarize Full Haplotype Enumeration on Genotype Matrix

EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci

plot.haplo.score.slide

Plot a haplo.score.slide Object

print.haplo.group

Print a haplo.group object

summary.haplo.em

Summarize contents of a haplo.em object

Simulated data for seqhap examples

anova.haplo.glm

Analysis of variance for haplo.glm model fit

Creates an object of class "locus"

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

Find Location from Mouse Clicks and Print Haplotypes on Plot

consistency checks for x.linked locus

score.sim.control

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

Compute Generalized Inverse of Input Matrix

Louis Information for haplo.glm

geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes

Haplotype Association Analysis in a Case-Control design

variance-covariance matrix of a fitted haplo.glm 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.

Power and sample size for the chi-square distribution

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

Plot a seqhap object

haplo.model.frame

Sets up a model frame for haplo.glm

print.haplo.score.merge

Print a haplo.score.merge object

Sequential Haplotype Scan Association Analysis for Case-Control Data

GLM Regression of Trait on Ambiguous Haplotypes

Set of haplotypes and frequencies for power and sample size calculations

print.haplo.score.slide

Print the contents of a haplo.score.slide object

Print a nice banner

find.haplo.beta.qt

Find beta coefficients for risk haplotypes, for specified r2

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

Frequencies for Haplotypes by Grouping Variable

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

Score Statistics for Association of Traits with Haplotypes

plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics

residuals.haplo.glm

Accessing residuals for haplo.glm fit