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.

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.