tidypopgen (version 0.4.3)

gt_as_plink: Export a gen_tibble object to PLINK bed format

Description

This function exports all the information of a gen_tibble object into a PLINK bed, ped or raw file (and associated files, i.e. .bim and .fam for .bed; .fam for .ped).

Usage

gt_as_plink(
  x,
  file = NULL,
  type = c("bed", "ped", "raw"),
  overwrite = TRUE,
  chromosomes_as_int = FALSE
)

Value

the path of the saved file

Arguments

x

a gen_tibble object

file

a character string giving the path to output file. If left to NULL, the output file will have the same path and prefix of the backingfile.

type

one of "bed", "ped" or "raw"

overwrite

boolean whether to overwrite the file.

chromosomes_as_int

boolean whether to use the integer representation of the chromosomes

Details

If the gen_tibble has been read in from vcf format, family.ID in the resulting plink files will be the same as sample.ID. If the gen_tibble has a grouping variable, this will be used as the family.ID in the resulting plink files. NOTE that writing to bed has been optimised for speed, but writing to ped or raw is slower, especially for large datasets.

Examples

example_gt <- load_example_gt("gen_tbl")

# Write a bed file
example_gt %>% gt_as_plink(type = "bed", file = paste0(tempfile(), "_plink"))

# Write a ped file
example_gt %>% gt_as_plink(type = "ped", file = paste0(tempfile(), "_plink"))

# Write a raw file
example_gt %>% gt_as_plink(type = "raw", file = paste0(tempfile(), "_plink"))