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.
- Install the latest development version from GitHub with
devtools::install_github("wegene-llc/radmixture")- Install the latest version on CRAN with
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')Pay attention:
Since the public datasets are not on CRAN, if you download this package from CRAN, you should download the datasets that you need from GitHub by yourself. For example:download.file(url = 'https://github.com/wegene-llc/radmixture/raw/master/data/globe4.alleles.RData', destfile = '/path/to/globe4.alleles.RData')
download.file(url = 'https://github.com/wegene-llc/radmixture/raw/master/data/globe4.4.F.RData', destfile = '/path/to/globe4.4.F.RData')And then, load them into R.
load('/path/to/globe4.alleles.RData')
load('/path/to/globe4.4.F.RData')Six public datasets could be used in this package.
- Use
tfrdpub()to transfer your raw data to a format understood by radmixture
# Use K4
res <- tfrdpub(genotype, 4, globe4.alleles, globe4.4.F)
# Use K7b
res <- tfrdpub(genotype, 7, K7b.alleles, K7b.7.F)
# Use world9
res <- tfrdpub(genotype, 9, world9.alleles, world9.9.F)
# Use E11
res <- tfrdpub(genotype, 11, e11.alleles, e11.11.F)
# Use K12b
res <- tfrdpub(genotype, 12, K12b.alleles, K12b.12.F)
# Use K13
res <- tfrdpub(genotype, 13, globe13.alleles, globe13.13.F)- Use
fFixQN()to calculate your result
# Use K4
ances <- fFixQN(res$g, res$q, res$f, tol = 1e-4, method = "BR", pubdata = "K4")
# Use K7b
ances <- fFixQN(res$g, res$q, res$f, tol = 1e-4, method = "BR", pubdata = "K7b")
# Use world9
ances <- fFixQN(res$g, res$q, res$f, tol = 1e-4, method = "BR", pubdata = "World9")
# Use E11
ances <- fFixQN(res$g, res$q, res$f, tol = 1e-4, method = "BR", pubdata = "E11")
# Use K12b
ances <- fFixQN(res$g, res$q, res$f, tol = 1e-4, method = "BR", pubdata = "K12b")
# Use K13
ances <- fFixQN(res$g, res$q, res$f, tol = 1e-4, method = "BR", pubdata = "K13")ances$q is your result.
- 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.
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.
MIT + LICENSE
- add tutorial