Reads PLINK tped and bed files

The function reads PLINK tped and bed files. radiator prefers the use of BED file. These files are converted to a connection SeqArray SeqArray GDS object/file of class SeqVarGDSClass (Zheng et al. 2017). The Genomic Data Structure (GDS) file format is detailed in gdsfmt.

Used internally in genometranslator and might be of interest for users.

Usage

read_plink(
  data,
  filename = NULL,
  parallel.core = parallel::detectCores() - 1,
  verbose = TRUE,
  ...
)

Arguments

data

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.

filename

(optional) The file name of the Genomic Data Structure (GDS) file. radiator will append .gds.rad to the filename. If the filename chosen exists in the working directory, the default radiator_datetime.gds is chosen. Default: filename = NULL.

parallel.core

Default: parallel.core = parallel::detectCores() - 1.

verbose

Logical indicating whether progress messages are emitted. Default: verbose = TRUE.

...

Additional arguments passed to lower-level readers, translators, or writers.

Value

For tped the function returns a list object with the non-modified tped and the strata corresponding to the tfam. With bed, the function returns a GDS object.

Details

Large PLINK files will require the use of BED plink format. Look below in the example for conversion with PLINK.

Large PLINK bed files will take longer to import and transform in GDS, but after the file is generated, you can close your computer and come back to it a month later and it's now a matter of sec to open a connection!

Dependencies

Required package dependencies are declared in DESCRIPTION and installed with genometranslator. Run genometranslator_dependencies() to inspect core packages, optional packages, and external executables.

Binary BED input uses the declared Bioconductor dependencies SeqArray and gdsfmt. The external PLINK executable is not required to read or write the supported PLINK formats.

References

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

Author

Thierry Gosselin thierrygosselin@icloud.com

Examples

if (FALSE) { # \dontrun{
data <- genometranslator::read_plink(data = "my_plink_file.bed")
# 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
} # }