README.md

In chenchunyu88/BATools: BATools: An R package that extends 'Bayesian Alphabet' for Whole Genome Prediction and Genome-wide association study

BATools

This package implements Bayesian model using Markov Chain Monte Carlo (MCMC) and Max a Posterior (MAP) algorithm for various Bayesian models for whole genome prediction (WGP) and genome-wide association (GWA).

The data in the demo is explained in https://github.com/chenchunyu88/batoolsdata/blob/master/MSUPRP.ipynb.

Warning:

The demo example is just showing how the packages is work, please refer to these papers appear in help(BATools) for previous study results how the prediction accuarcy and GWA can be affected by different factors. In order for MCMC to convergence, change number of iteration and burn-In to 100,000 or greater depending on the size of your data.

The package is under developement, but it is functional.

To install the package you can follow the steps (recommended: use Rstudio to run this):

install.packages("devtools")

library(devtools)

devtools::install_github("hadley/devtools")

devtools::install_github("chenchunyu88/BATools")

Or, you can download it as an .zip file and use R CMD INSTALL BATools to install it in the command line.

A quick introduction: vignette("BATools")

Help can be accessed by typing: help(BATools), help(bafit)

Example codes can be found in demo/ folder.

chenchunyu88/BATools documentation built on May 19, 2019, 8:21 a.m.