Learn R Programming

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

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.

seqhap

Sequential haplotype scan methods to perform association analyses for case-control data. When evaluating each locus, loci that contribute additional information to haplotype associations with disease status will be added sequentially.

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.

Copy Link

Version

Install

install.packages('haplo.stats')

Monthly Downloads

1,909

Version

1.9.5.1

License

GPL (>= 2)

Maintainer

Jason Sinnwell

Last Published

February 2nd, 2024

Functions in haplo.stats (1.9.5.1)

haplo.em.fitter

Compute engine for haplotype EM algorithm
haplo.glm.control

Create list of control parameters for haplo.glm
haplo.cc

Haplotype Association Analysis in a Case-Control design
haplo.model.frame

Sets up a model frame for haplo.glm
haplo.hash

Integer Rank Codes for Haplotypes
haplo.group

Frequencies for Haplotypes by Grouping Variable
haplo.em.control

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

EM Computation of Haplotype Probabilities, with Progressive Insertion of Loci
haplo.glm

GLM Regression of Trait on Ambiguous Haplotypes
haplo.scan

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

Score Statistics for Association of Traits with Haplotypes
haplo.power.cc

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

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

Louis Information for haplo.glm
print.haplo.em

Print contents of a haplo.em object
haplo.design

Build a design matrix for haplotypes
print.haplo.group

Print a haplo.group object
haplo.score.slide

Score Statistics for Association of Traits with Haplotypes
haplo.score.merge

Merge haplo.score And haplo.group Objects
seqhap.dat

Simulated data for seqhap examples
na.geno.keep

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

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

consistency checks for x.linked locus
plot.haplo.score

Plot Haplotype Frequencies versus Haplotype Score Statistics
plot.haplo.score.slide

Plot a haplo.score.slide Object
locator.haplo

Find Location from Mouse Clicks and Print Haplotypes on Plot
plot.seqhap

Plot a seqhap object
summary.haplo.em

Summarize contents of a haplo.em object
score.sim.control

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

Creates an object of class "locus"
print.haplo.cc

Print a haplo.cc object
printBanner

Print a nice banner
residuals.haplo.glm

Accessing residuals for haplo.glm fit
summary.haplo.glm

Print and summary of a haplo.glm object
hla.demo

HLA Loci and Serologic Response to Measles Vaccination
seqhap

Sequential Haplotype Scan Association Analysis for Case-Control Data
print.haplo.score.slide

Print the contents of a haplo.score.slide object
print.haplo.score.merge

Print a haplo.score.merge object
dglm.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.
print.haplo.scan

Print a haplo.scan object
summaryGeno

Summarize Full Haplotype Enumeration on Genotype Matrix
vcov.haplo.glm

variance-covariance matrix of a fitted haplo.glm object
print.haplo.score

Print a haplo.score object
Ginv

Compute Generalized Inverse of Input Matrix
get.hapPair

Get a list of objects for haplotype pairs
geno.count.pairs

Counts of Total Haplotype Pairs Produced by Genotypes
geno1to2

convert genotype matrix from 1-column 2-column
fitted.haplo.glm

Fitted values from haplo.glm fit
find.haplo.beta.qt

Find beta coefficients for risk haplotypes, for specified r2
hapPower.demo

Set of haplotypes and frequencies for power and sample size calculations
anova.haplo.glm

Analysis of variance for haplo.glm model fit
chisq.power

Power and sample size for the chi-square distribution
f.power

Power and sample size for the F distribution