Used internally in radiator to detect the file format

Source: R/detect_genomic_format.R

Detect the file format of genomic data set.

detect_genomic_format(data, guess = NULL)

Arguments

data

15 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). New addition to radiator: the Apache Parquet columnar storage file format that will replace the fst (Lightning Fast Serialiation) format. Documented in Input genomic datasets of tidy_genomic_data.

guess

(character) In development, guess faster the type of file. Default: guess = NULL.

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.

  • arrow parquet: for a Apache Parquet columnar storage file format, used by arrow R package.

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
#To verify your file is detected by radiator as the correct format:
radiator::detect_genomic_format(data = "populations.snps.vcf")
} # }