In wegene-llc/radmixture: Calculate Population Stratification

This is an introduction to radmixture which could help you with estimating individual ancestries from large SNP genotype data.

This document introduces you how to use this package.

Installation

• Install the latest development version from github with

devtools::install_github("wegene-llc/radmixture")

• Install the latest version from CRAN

install.packages("radmixture")

First, you must prepare your raw data file as follow:

and read it into R with read.table or read.csv.

library(radmixture)
genotype <- read.table(file = '/path/to/file')
# genotype <- read.csv(file = 'path/to/file')

Calculate your ancestry components with public dataset

Example

• Use tfrdpub()to transfer your raw data to a format understood by radmixture

res <- tfrdpub(genotype, 13, global13.alleles, global13.13.F)

• Calculate

ances <- fFixQN(res$g, res$q, res$f, tol = 1e-4, method = 'BR', pubdata = "K13")

ances$q is your K13 result.

References

• D.H. Alexander, J. Novembre, and K. Lange. Fast model-based estimation of ancestry in unrelated individuals. Genome Research, 19:1655–1664, 2009.
• H. Zhou, D. H. Alexander, and K. Lange. A quasi-Newton method for accelerating the convergence of iterative optimization algorithms. Statistics and Computing, 2009.

Contributions

We welcome contributions on radmixture. You can fork this repo and make your changes and submit a pull request. Report bug issues on issue page.

License

MIT + LICENSE

TODO

• Add tutorial for radmixture

wegene-llc/radmixture documentation built on May 4, 2019, 2:06 a.m.