Saves genotype and map data from an SNPDataLong object in PLINK format (.ped/.map and optionally binary files).
savePlink(
object,
path,
name = "plink_data",
run_plink = TRUE,
chunk_size = 1000,
extra_args = NULL
)An object of class SNPDataLong.
Character. Directory where files will be saved. Must be supplied
by the caller (e.g. a folder inside tempdir() for examples).
Character. Base name for PLINK output files.
Logical. If TRUE (default), runs PLINK1 to convert to binary files. If FALSE, only .ped and .map files are saved.
Integer. Number of individuals per chunk for writing .ped file (default: 1000).
Character vector. Extra arguments appended verbatim to the
PLINK command line when run_plink = TRUE. Useful for non-human data;
e.g. "--chr-set 29" makes PLINK treat autosomes 1-29 correctly for
cattle instead of reading 23-26 as human X/Y/XY/MT. Default is NULL.
No return value, called for side effects. Files (.ped/.map,
and .bed/.bim/.fam when run_plink = TRUE) are
written under path.
# \donttest{
set.seed(1)
raw_mat <- matrix(as.raw(sample(1:3, 100, TRUE)), nrow = 10, ncol = 10)
rownames(raw_mat) <- paste0("S", 1:10)
colnames(raw_mat) <- paste0("SNP", 1:10)
geno <- methods::new("SnpMatrix", raw_mat)
obj <- methods::new("SNPDataLong",
geno = geno,
map = data.frame(Name = colnames(geno),
Chromosome = 1,
Position = 1:10),
path = tempfile(),
xref_path = "chip1")
savePlink(obj, path = tempdir(), name = "demo",
run_plink = FALSE, chunk_size = 5)
#>
#> +====================================+
#> | Saving Files in Plink Format |
#> +====================================+
#> Writing .ped file in chunks...
#> Wrote individuals 1 to 5
#> Wrote individuals 6 to 10
#> .ped file written: /tmp/Rtmp4EiFZk/demo.ped
#> Writing .map file...
#> .map file written: /tmp/Rtmp4EiFZk/demo.map
#> Skipping PLINK binary conversion as requested.
#> All done.
# }