R: An Interface for Running 'ADMIXTOOLS' Analyses

# An Interface for Running 'ADMIXTOOLS' Analyses

## Documentation for package ‘admixr’ version 0.9.2

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

count_snps | Count the number/proportion of present/missing sites in each sample
d | Calculate the D, f4, f4-ratio, or f3 statistic.
download_data | Download example SNP data.
eigenstrat | EIGENSTRAT data constructor
f3 | Calculate the D, f4, f4-ratio, or f3 statistic.
f4 | Calculate the D, f4, f4-ratio, or f3 statistic.
f4ratio | Calculate the D, f4, f4-ratio, or f3 statistic.
filter_bed | Filter EIGENSTRAT data based on a given BED file
loginfo | Print the full log output of an admixr wrapper to the console.
merge_eigenstrat | Merge two sets of EIGENSTRAT datasets
print.admixr_result | Print out the admixr result object (dataframe or a list) without showing the hidden attributes.
print.EIGENSTRAT | EIGENSTRAT print method
qpAdm | 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)
qpWave | Find the most likely number of ancestry waves using the qpWave method.
read_geno | Read an EIGENSTRAT ind/snp/geno file.
read_ind | Read an EIGENSTRAT ind/snp/geno file.
read_output | Read an output file from one of the ADMIXTOOLS programs.
read_snp | Read an EIGENSTRAT ind/snp/geno file.
relabel | Change labels of populations or samples
reset | Reset modifications to an EIGENSTRAT object
transversions_only | Remove transversions (C->T and G->A substitutions)
write_geno | Write an EIGENSTRAT ind/snp/geno file.
write_ind | Write an EIGENSTRAT ind/snp/geno file.
write_snp | Write an EIGENSTRAT ind/snp/geno file.