Package: admixr 0.9.2.9000

Martin Petr

admixr: An Interface for the Software Package 'ADMIXTOOLS'

An interface for various command-line tools provided by the software suite 'ADMIXTOOLS' (<https://github.com/DReichLab/AdmixTools>). Wrapper functions completely automate the generation of intermediate configuration files, run 'ADMIXTOOLS' programs on the command-line in the background, and extract statistics of interest from plain-text files which they produce. This allows users to avoid dealing with low-level technical details of shell scripting (which is requried by traditional 'ADMIXTOOLS' workflows) and focus on their research problem at hand instead. A set of complementary functions for processing and filtering of data in the 'EIGENSTRAT' format is also provided.

Authors:Martin Petr [aut, cre]

admixr_0.9.2.9000.tar.gz
admixr_0.9.2.9000.zip(r-4.7)admixr_0.9.2.9000.zip(r-4.6)admixr_0.9.2.9000.zip(r-4.5)
admixr_0.9.2.9000.tgz(r-4.6-any)admixr_0.9.2.9000.tgz(r-4.5-any)
admixr_0.9.2.9000.tar.gz(r-4.7-any)admixr_0.9.2.9000.tar.gz(r-4.6-any)
admixr_0.9.2.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
admixr/json (API)

# Install 'admixr' in R:
install.packages('admixr', repos = c('https://bodkan.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/bodkan/admixr/issues

On CRAN:

Conda:

bioinformaticspopgenpopulation-genetics

7.55 score 37 stars 95 scripts 367 downloads 5 mentions 25 exports 28 dependencies

Last updated from:5def1e935e. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK130
source / vignettesOK192
linux-release-x86_64OK132
macos-release-arm64OK156
macos-oldrel-arm64OK174
windows-develOK70
windows-releaseOK82
windows-oldrelOK74
wasm-releaseOK117

Exports:%>%count_snpsddownload_dataeigenstratf3f4f4ratiofilter_bedloginfomerge_eigenstratqpAdmqpAdm_filterqpAdm_rotationqpWaveread_genoread_indread_outputread_snprelabelresettransversions_onlywrite_genowrite_indwrite_snp

Dependencies:bitbit64clicliprcpp11crayondplyrgenericsgluehmslifecyclemagrittrpillarpkgconfigprettyunitsprogressR6readrrlangstringistringrtibbletidyselecttzdbutf8vctrsvroomwithr

Basic overview of the admixr package
Introduction | Installation | A note about EIGENSTRAT format | ind file | snp file (first 3 lines) | geno file (first 3 lines) | Philosophy of admixr | Internal representation of EIGENSTRAT data | D statistic | f4 statistic | f4-ratio statistic | f3 statistic | qpWave and qpAdm | qpWave | qpAdm | Grouping samples | Counting present/missing SNPs | Data filtering | Filtering based on a BED file | Filtering out potential ancient DNA damage SNPs | Merging EIGENSTRAT datasets | Examining log information
Rendered fromvignette-01-tutorial.Rmdusingknitr::rmarkdown

Last update: 2025-11-24
Started: 2024-05-10

Running qpAdm models with the 'rotation' strategy
Introduction | qpAdm "rotation" | Implementation in admixr | Concrete example | Performing exhaustive search by rotating sources/outgroups | Examining and filtering fitted models | Conclusions | Final remarks
Rendered fromvignette-02-qpAdm.Rmdusingknitr::rmarkdown

Last update: 2025-11-24
Started: 2024-05-10