Transform bi-allelic PLINK files in .tped or .bed formats
into a tidy dataset.
Used internally in radiator and assigner and might be of interest for users.
tidy_plink(
data,
parallel.core = parallel::detectCores() - 1,
verbose = FALSE,
...
)The PLINK file.
bi-allelic data only. For haplotypes use VCF.
tped file format: the corresponding tfam file must be in the directory.
bed file format: IS THE PREFERRED format, the corresponding
fam and bim files must be in the directory.
(optional) The number of core used for parallel
execution during import.
Default: parallel.core = parallel::detectCores() - 1.
(optional, logical) When verbose = TRUE
the function is a little more chatty during execution.
Default: verbose = TRUE.
(optional) Advance mode that allows to pass further arguments for fine-tuning the function. Also used for legacy arguments (see details or special section)
A tidy tibble of the PLINK file.
dots-dots-dots ... allows to pass several arguments for fine-tuning the function:
calibrate.alleles: logical. For tped files, if
calibrate.alleles = FALSE the function runs faster
but REF/ALT alleles may not be calibrated. The default assumes the users or
sotware producing the PLINK file calibrated the alleles.
Default: calibrate.alleles = FALSE.
Zheng X, Gogarten S, Lawrence M, Stilp A, Conomos M, Weir BS, Laurie C, Levine D (2017). SeqArray – A storage-efficient high-performance data format for WGS variant calls. Bioinformatics.
PLINK: a tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics. 2007: 81: 559–575. doi:10.1086/519795
if (FALSE) { # \dontrun{
data <- radiator::tidy_plink(data = "my_plink_file.bed", verbose = TRUE)
# when conversion is required from TPED to BED, in Terminal:
# plink --tfile my_plink_file --make-bed --allow-no-sex --allow-extra-chr --chr-set 95
} # }