BVS: Bayesian Variant Selection: Bayesian Model Uncertainty Techniques for Genetic Association Studies

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The functions in this package focus on analyzing case-control association studies involving a group of genetic variants. In particular, we are interested in modeling the outcome variable as a function of a multivariate genetic profile using Bayesian model uncertainty and variable selection techniques. The package incorporates functions to analyze data sets involving common variants as well as extensions to model rare variants via the Bayesian Risk Index (BRI) as well as haplotypes. Finally, the package also allows the incorporation of external biological information to inform the marginal inclusion probabilities via the iBMU.

Author
Melanie Quintana <maw27.wilson@gmail.com>
Date of publication
2012-08-09 17:07:48
Maintainer
Melanie Quintana <maw27.wilson@gmail.com>
License
Unlimited
Version
4.12.1

View on CRAN

Man pages

BVS-package
Bayesian Variant Selection: Bayesian Model Uncertainty...
enumerateBVS
Function to Enumerate all models for Bayesian Variant...
fitBVS
Function to calculate fitness for each model for Bayesian...
hapBVS
Function to estimate and report a set of haplotypes given a...
InformBVS.I.out
Example Output From 100K iterations of sampleBVS with...
InformBVS.NI.out
Example Output From 100K iterations of sampleBVS with...
InformData
PNAT Study-based Simulation: Informative Data.
Informresults.I
Example Summary From 100K iterations of sampleBVS with...
Informresults.NI
Example Summary From 100K iterations of sampleBVS with...
plotRVS
Image Plots for top Variant and Region Inclusions
RareBVS.out
Example Output From 100K iterations of sampleBVS with Rare...
RareData
Simulated Example Rare Variant data set.
RareResults
Example Summary From 100K iterations of sampleBVS with Rare...
sampleBVS
Sampling Algorithm for Bayesian Variant Selection Methods
summaryBVS
Calculates Posterior Summaries for BVS Methods

Files in this package

BVS
BVS/MD5
BVS/R
BVS/R/summaryBVS.R
BVS/R/sampleBVS.R
BVS/R/plotBVS.R
BVS/R/hapBVS.R
BVS/R/fitBVS.R
BVS/R/enumerateBVS.R
BVS/NAMESPACE
BVS/man
BVS/man/summaryBVS.Rd
BVS/man/sampleBVS.Rd
BVS/man/RareResults.Rd
BVS/man/RareData.Rd
BVS/man/RareBVS.out.Rd
BVS/man/plotRVS.Rd
BVS/man/Informresults.NI.Rd
BVS/man/Informresults.I.Rd
BVS/man/InformData.Rd
BVS/man/InformBVS.NI.out.Rd
BVS/man/InformBVS.I.out.Rd
BVS/man/hapBVS.Rd
BVS/man/fitBVS.Rd
BVS/man/enumerateBVS.Rd
BVS/man/BVS-package.Rd
BVS/DESCRIPTION
BVS/data
BVS/data/RareResults.rda
BVS/data/RareData.rda
BVS/data/RareBVS.out.rda
BVS/data/Informresults.NI.rda
BVS/data/Informresults.I.rda
BVS/data/InformData.rda
BVS/data/InformBVS.NI.out.rda
BVS/data/InformBVS.I.out.rda
BVS/data/datalist
BVS/ChangeLog