README.md

In radamsRHA/ThetaMater: ThetaMater: Bayesian estimation of the population size parameter theta from genomic data

ThetaMater: Rapid and scalable Bayesian estimation of the population size parameter theta=4Nu from diverse genetic data

NOTE See the file https://github.com/radamsRHA/ThetaMater/tree/master/vignettes for detailed instructions

Steps for Bayesian estimation of theta and alpha (see tutorial for more details)

1. Read input files and convert to infinite-sites data used by ThetaMater
2. Choose a specific Bayesian model for estimating theta along (ThetaMater.M1), theta with a fixed alpha shape parameter (ThetaMater.M2), or the joint posterior distribution of theta and alpha (ThetaMater.M3).
3. (Optional) Convert the results of ThetaMater into estimates of effective population size by multiplying the posterior distribution of theta by a given mutation rate.
4. (Optional) Filter out loci with high mutation counts that likely represent spurious loci using the posterior predictive simulator function (ThetaMater.PPS).
5. (Optional) Identifying the maximum bounds of mutation counts from the posterior distribution, remove loci with outlier mutation counts that are too high beyond the posterior distribution, and re-estimate Theta using filtered dataset

Installing R package GppFst from github

IMPORTANT: Please make sure that the most recent version of Rcpp is installed. You can use this command to install it: install_github("https://github.com/RcppCore/Rcpp")

ThetaMater require the Boost c++ libraries to be installed for the fast calculation of the underlying likelihood functions. I recommend install the Boost libraries using brew for Mac systems (brew install boost). The latest version of the Boost c++ libraries here: https://www.boost.org. You can also install boost libraries by installing brew and using the command brew update and then brew install boost

The R package ThetaMater is freely available to download and distribute from github https://github.com/radamsRHA/ThetaMater/. To install and load ThetaMater, you must first install the R packages devtools, Rcpp, and MCMCpack. Additionally, make sure the most updated version of R version 3.3.3 is installed (see above warning). Download R version 3.3.3 here: https://cran.r-project.org/bin/macosx/.

install.packages("devtools")
install.packages("MCMCpack")
install_github("https://github.com/RcppCore/Rcpp")

Now using devtools we can install ThetaMater from github:

library(devtools)
install_github("radamsRHA/ThetaMater")
library(ThetaMater) # Load package ThetaMater
library(MCMCpack) # Load dependancy phybase

To begin using ThetaMater try using our vignette with example files provided with this package.

radamsRHA/ThetaMater documentation built on April 25, 2024, 10:11 a.m.