Learn R Programming

⚠️There's a newer version (1.9.7) of this package.Take me there.

haplo.stats (version 1.7.7)

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.

Copy Link

Version

Install

install.packages('haplo.stats')

Monthly Downloads

1,954

Version

1.7.7

License

GPL (>= 2)

Maintainer

Jason Sinnwell

Last Published

April 6th, 2016

Functions in haplo.stats (1.7.7)

find.haplo.beta.qt

Find beta coefficients for risk haplotypes, for specified r2

fitted.haplo.glm

Fitted values from haplo.glm fit

print.haplo.scan

Print a haplo.scan object

haplo.em.control

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

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

convert genotype matrix from 1-column 2-column

HLA Loci and Serologic Response to Measles Vaccination

score.sim.control

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

print.haplo.score.slide

Print the contents of a haplo.score.slide object

Creates an object of class "locus"

Power and sample size for the chi-square distribution

residuals.haplo.glm

Accessing residuals for haplo.glm fit

Integer Rank Codes for Haplotypes

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

haplo.score.slide

Score Statistics for Association of Traits with Haplotypes

haplo.score.merge

Merge haplo.score And haplo.group Objects

print.haplo.group

Print a haplo.group object

Plot a seqhap object

plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics

Get a list of objects for haplotype pairs

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

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

anova.haplo.glm

Analysis of variance for haplo.glm model fit

GLM Regression of Trait on Ambiguous Haplotypes

plot.haplo.score.slide

Plot a haplo.score.slide Object

print.haplo.score.merge

Print a haplo.score.merge object

Print a haplo.cc object

Sequential Haplotype Scan Association Analysis for Case-Control Data

Score Statistics for Association of Traits with Haplotypes

Simulated data for seqhap examples

Find Location from Mouse Clicks and Print Haplotypes on Plot

variance-covariance matrix of a fitted haplo.glm object

Power and sample size for the F distribution

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.glm

Print and summary of a haplo.glm object

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

haplo.model.frame

Sets up a model frame for haplo.glm

print.haplo.score

Print a haplo.score object

Haplotype Association Analysis in a Case-Control design

Compute Generalized Inverse of Input Matrix

consistency checks for x.linked locus

summary.haplo.em

Summarize contents of a haplo.em object

haplo.glm.control

Create list of control parameters for haplo.glm

Set of haplotypes and frequencies for power and sample size calculations

Frequencies for Haplotypes by Grouping Variable

Print contents of a haplo.em object

Print a nice banner

EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci

geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes

Summarize Full Haplotype Enumeration on Genotype Matrix

Louis Information for haplo.glm

Build a design matrix for haplotypes

haplo.em.fitter

Compute engine for haplotype EM algorithm