Convert a gentibble to a .geno file for sNMF from the LEA package

This function writes a .geno file from a gen_tibble. Unless a file path is given, a file with suffix .geno is written in the same location as the .rds and .bk files that underpin the gen_tibble.

Usage

gt_as_geno_lea(x, file = NULL)

Arguments

x: a gen_tibble
file: the .geno filename with a path, or NULL (the default) to use the location of the backing files.

Value

the path of the .geno file

Details

NOTE that we currently read all the data into memory to write the file, so this function is not suitable for very large datasets.

Note

the .geno format only supports haploid or diploid data, so this function only works on diploid (or pseudohaploid) gen_tibble objects. Pseudohaploid data is simply treated as regular diploid genotype counts (dosage 0/2), the same convention used by other tools (e.g. PLINK).

Examples

example_gt <- load_example_gt("gen_tbl")

# Write a geno file
gt_as_geno_lea(example_gt, file = paste0(tempfile(), "_example.geno"))
#> [1] "/tmp/RtmpqbnViX/file29bc7a7bfae7_example.geno"