Table 2 The required format of datasets and import functions of geneHapR

Genotype (necessary)

VCF: *.vcf, *.vcf.gz;

FASTA: *.fa, *.fasta;

P.link: (*.ped & *.map);

hmp: *.hmp;

table: *.txt, *.csv

import_vcf();

import_seqs();

import_plink.pedmap();

import_hmp();

read.table(), read.csv()

Annotation (optional)

GFF: *.gff, *.gff3,

BED4/BED6: *.bed

import_gff();

import_bed()

Accession information (optional)

table: *.txt, *.csv

read.table(), read.csv()