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admixr

An Interface for Running 'ADMIXTOOLS' Analyses

An interface for performing all stages of 'ADMIXTOOLS' analyses (<https://reich.hms.harvard.edu/software>) entirely from R. Wrapper functions (D, f4, f3, etc.) completely automate the generation of intermediate configuration files, run 'ADMIXTOOLS' programs on the command-line, and parse output files to extract values of interest. This allows users to focus on the analysis itself instead of worrying about low-level technical details. A set of complementary functions for processing and filtering of data in the 'EIGENSTRAT' format is also provided.

Functions (21)

Count the number/proportion of present/missing sites in each sample

download_data

Download example SNP data.

EIGENSTRAT data constructor

Calculate the D, f4, f4-ratio, or f3 statistic.

Filter EIGENSTRAT data based on a given BED file

keep_transitions

Remove transversions (C->T and G->A substitutions)

Print the full log output of an admixr wrapper to the console.

merge_eigenstrat

Merge two sets of EIGENSTRAT datasets

pipe

Pipe operator

print.EIGENSTRAT

EIGENSTRAT print method

print.admixr_result

Print out the admixr result object (dataframe or a list) without showing the hidden attributes.

Calculate ancestry proportions in a set of target populations.

qpAdm_filter

Filter qpAdm rotation results for only 'sensible' models

qpAdm_rotation

Fit qpAdm models based on the rotation strategy described in Harney et al. 2020 (bioRxiv)

Find the most likely number of ancestry waves using the qpWave method.

Read an EIGENSTRAT ind/snp/geno file.

read_output

Read an output file from one of the ADMIXTOOLS programs.

Change labels of populations or samples

Reset modifications to an EIGENSTRAT object

transversions_only

Remove transversions (C->T and G->A substitutions)

Write an EIGENSTRAT ind/snp/geno file.

admixr

An Interface for Running 'ADMIXTOOLS' Analyses

v0.9.1

MIT + file LICENSE

Authors

Martin Petr [aut, cre] (<https://orcid.org/0000-0003-4879-8421>)

Initial release

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