Learn R Programming

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

haplo.stats (version 1.4.4)

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

Description

A suite of S-PLUS/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.

Copy Link

Version

Install

install.packages('haplo.stats')

Monthly Downloads

1,656

Version

1.4.4

License

GPL-2 | file LICENSE

Maintainer

Jason Sinnwell

Last Published

October 1st, 2009

Functions in haplo.stats (1.4.4)

Power and sample size for the chi-square distribution

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

Score Statistics for Association of Traits with Haplotypes

Set up an example dataset provided within the library.

Set of haplotypes and frequencies for power and sample size calculations

convert genotype matrix from 1-column 2-column

Simulated data for seqhap examples

Compute Generalized Inverse of Input Matrix

haplo.score.slide

Score Statistics for Association of Traits with Haplotypes

Haplotype Association Analysis in a Case-Control design

print.haplo.score

Print a haplo.score object

haplo.em.fitter

Compute engine for haplotype EM algorithm

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

Power and sample size for the F distribution

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

Sequential Haplotype Scan Association Analysis for Case-Control Data

print.haplo.glm

Print a contents of a haplo.glm object

Plot a seqhap object

Print contents of a haplo.em object

print.haplo.group

Print a haplo.group object

Print a nice banner

plot.haplo.score.slide

Plot a haplo.score.slide Object

Print a haplo.cc object

consistency checks for x.linked locus

HLA Loci and Serologic Response to Measles Vaccination

print.haplo.score.slide

Print the contents of a haplo.score.slide object

EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci

Creates an object of class "locus"

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

Summarize Full Haplotype Enumeration on Genotype Matrix

haplo.score.merge

Merge haplo.score And haplo.group Objects

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

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.

Integer Rank Codes for Haplotypes

print.haplo.scan

Print a haplo.scan object

Get a list of objects for haplotype pairs

Frequencies for Haplotypes by Grouping Variable

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

score.sim.control

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

plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics

print.haplo.score.merge

Print a haplo.score.merge object

summary.haplo.em

Summarize contents of a haplo.em object

Find Location from Mouse Clicks and Print Haplotypes on Plot

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

find.haplo.beta.qt

Find beta's for risk haplotypes, for specified r2

Louis Information for haplo.glm

Build a design matrix for haplotypes

Print Contents of a Seqhap Object

geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes

haplo.glm.control

Create list of control parameters for haplo.glm

haplo.model.frame

Sets up a model frame for haplo.glm

GLM Regression of Trait on Ambiguous Haplotypes