An Interface for Running 'ADMIXTOOLS' Analyses

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Documentation for package ‘admixr’ version 0.9.1

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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