Package index

Admixture statistics

f4ratio() d() f4() f3()

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

qpWave()

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

qpAdm()

Calculate ancestry proportions in a set of target populations.

qpAdm model exploration

qpAdm_rotation()

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

qpAdm_filter()

Filter qpAdm rotation results for only 'sensible' models

Examining output log information

loginfo()

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

Data processing and filtering

eigenstrat()

EIGENSTRAT data constructor

filter_bed()

Filter EIGENSTRAT data based on a given BED file

transversions_only()

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

relabel()

Change labels of populations or samples

reset()

Reset modifications to an EIGENSTRAT object

merge_eigenstrat()

Merge two sets of EIGENSTRAT datasets

count_snps()

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

Reading/writing EIGENSTRAT data

read_ind() read_snp() read_geno()

Read an EIGENSTRAT ind/snp/geno file.

write_ind() write_snp() write_geno()

Write an EIGENSTRAT ind/snp/geno file.

read_output()

Read an output file from one of the ADMIXTOOLS programs.

Utility functions

download_data()

Download example SNP data.

print(<EIGENSTRAT>)

EIGENSTRAT print method

print(<admixr_result>)

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