. 2023 May 15;24:199. doi: 10.1186/s12859-023-05318-9

Table 2.

The required format of datasets and import functions of geneHapR

Datasets	Input file format	Import function
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()

Datasets

Input file format

Import function

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()