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

Share:

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.

Author
Raquel Iniesta and Victor Moreno
Date of publication
2013-03-13 21:25:31
Maintainer
Raquel Iniesta <riniesta@pssjd.org>
License
GPL (>= 2)
Version
1.0.1

View on CRAN

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

Files in this package

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