detect_genomic_format: Used internally in radiator to detect the file format

In thierrygosselin/radiator: RADseq Data Exploration, Manipulation and Visualization using R

Used internally in radiator to detect the file format

Description

Detect file format of genomic data set.

Usage

detect_genomic_format(data)

Arguments

data

14 options for input: VCFs (SNPs or Haplotypes, to make the vcf population ready), plink (tped and bed), stacks haplotype file, genind (library(adegenet)), genlight (library(adegenet)), gtypes (library(strataG)), genepop, DArT, and a data frame in long/tidy or wide format. To verify that radiator detect your file format use detect_genomic_format (see example below). Documented in Input genomic datasets of tidy_genomic_data.

Value

One of these file format:

• tbl_df: for a data frame

• genind: for a genind object

• genlight: for a genlight object

• gtypes: for a gtypes object

• vcf.file: for a vcf file

• plink.tped.file: for a plink tped file

• plink.bed.file: for a plink bed file

• genepop.file: for a genepop file

• haplo.file: for a stacks haplotypes file

• fstat.file: for a fstat file

• dart: for a DArT file

• fst.file: for a file ending with .rad

• SeqVarGDSClass: for SeqArray GDS file.

Author(s)

Thierry Gosselin [e-mail]

Examples

## Not run: 
#To verify your file is detected by radiator as the correct format:
radiator::detect_genomic_format(data = "populations.snps.vcf")

## End(Not run)

thierrygosselin/radiator documentation built on Nov. 7, 2024, 1:30 p.m.