BayHap: Bayesian analysis of haplotype association using Markov Chain Monte Carlo
Version 1.0.1

The package BayHap performs simultaneous estimation of uncertain haplotype frequencies and association with haplotypes based on generalized linear models for quantitative, binary and survival traits. Bayesian statistics and Markov Chain Monte Carlo techniques are the theoretical framework for the methods of estimation included in this package. Prior values for model parameters can be included by the user. Convergence diagnostics and statistical and graphical analysis of the sampling output can be also carried out.

AuthorRaquel Iniesta and Victor Moreno
Date of publication2013-03-13 21:25:31
MaintainerRaquel Iniesta <riniesta@pssjd.org>
LicenseGPL (>= 2)
Version1.0.1
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("BayHap")

Getting started

Package overview

Popular man pages

autocorr: Autocorrelation Function
BayHap-internal: Internal BayHap functions
BIC: Bayesian Information Criterion
conv.test: Heidelberger and Welch Convergence Diagnostics
plotRmean: Plot Running Mean of the Parameter Estimation
plotTrace: Plot Trace Histories
setupData: Check and prepares original data to be analyzed
See all...

All man pages Function index File listing

Man pages

autocorr: Autocorrelation Function
bayhapFreq: Estimation of haplotype frequencies
BayHap-internal: Internal BayHap functions
BayHap-package: Bayesian analysis of haplotype association using MCMC
bayhapReg: Bayesian analysis of haplotype association using Markov Chain...
BIC: Bayesian Information Criterion
conv.test: Heidelberger and Welch Convergence Diagnostics
correl: Correlation Matrix
haplo.prior: Prior values for model parameters
plotACF: Plot autocorrelation function
plotDensity: Plot Density Functions
plotFreq: Plot acf, running mean, density functions and trace histories
plotReg: Plot acf, running mean, density functions and trace histories
plotRmean: Plot Running Mean of the Parameter Estimation
plotTrace: Plot Trace Histories
setupData: Check and prepares original data to be analyzed

Functions

BIC Man page
BayHap Man page
BayHap-package Man page
allele Man page Source code
allele.names Man page Source code
autocorr Man page
bayhapFreq Man page
bayhapReg Man page
boa.plot.acf.ad Man page
chain.import Man page
combinations Man page
conv.test Man page
correl Man page
expectedGenotypes Man page
genotype Man page Source code
haplo.list Man page
haplo.list.all Man page
haplo.pairs Man page Source code
haplo.prior Man page Source code
import Man page
is.genotype Man page
is.locus Man page
is.snp Man page
make.dummies Man page
permutations Man page
plotACF Man page
plotDensity Man page
plotFreq Man page
plotReg Man page
plotRmean Man page
plotTrace Man page
print.freq Man page
print.reg Man page Source code
setupData Man page
survival Man page

Files

MD5
src
src/mcmc.c
man
man/setupData.Rd
man/plotTrace.Rd
man/plotRmean.Rd
man/plotReg.Rd
man/plotFreq.Rd
man/plotDensity.Rd
man/plotACF.Rd
man/haplo.prior.Rd
man/correl.Rd
man/conv.test.Rd
man/bayhapReg.Rd
man/bayhapFreq.Rd
man/autocorr.Rd
man/BayHap-package.Rd
man/BayHap-internal.Rd
man/BIC.Rd
R
R/survival.R
R/setupData.R
R/print.reg.R
R/print.freq.R
R/plotTrace.R
R/plotRmean.R
R/plotReg.R
R/plotFreq.R
R/plotDensity.R
R/plotACF.R
R/permutations.R
R/make.dummies.R
R/is.snp.R
R/is.locus.R
R/is.genotype.R
R/import.R
R/haplo.prior.R
R/haplo.pairs.R
R/haplo.list.all.R
R/haplo.list.R
R/genotype.R
R/expectedGenotypes.R
R/correl.R
R/conv.test.R
R/combinations.R
R/chain.import.R
R/boa.plot.acf.ad.R
R/bayhapReg.R
R/bayhapFreq.R
R/autocorr.R
R/allele.names.R
R/allele.R
R/BayHap-internal.R
R/BIC.R
NAMESPACE
DESCRIPTION
BayHap documentation built on May 19, 2017, 12:55 p.m.

Questions? Problems? Suggestions? Tweet to @rdrrHQ or email at ian@mutexlabs.com.

Please suggest features or report bugs in the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.