pgen2gds: Format Conversion between PLINK2 PGEN and GDS

GNU General Public License, GPLv3

Description

This package provides functions for format conversion from PLINK2 pgen files to SeqArray GDS files, and from SeqArray GDS files to PLINK2 pgen files.

Version

v0.99.4

Package Maintainer

Dr. Xiuwen Zheng

Installation

Requires R (≥ v4.0.0), gdsfmt, SeqArray

• Installation from Biocondutor:

if (!requireNamespace("BiocManager", quietly=TRUE))
    install.packages("BiocManager")
BiocManager::install("pgen2gds")

• Installation from Github:

library(remotes)
install_github("zhengxwen/pgen2gds")

The install_github() approach requires that you build from source, i.e. make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

Citations for GDS

Zheng X, Levine D, Shen J, Gogarten SM, Laurie C, Weir BS (2012). A High-performance Computing Toolset for Relatedness and Principal Component Analysis of SNP Data. Bioinformatics. DOI: 10.1093/bioinformatics/bts606.

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. DOI: 10.1093/bioinformatics/btx145.

Examples

library(pgen2gds)

# Example file
pgen_fn <- system.file("extdata", "plink2_gen.pgen", package="pgen2gds")

# Format conversion
seqPGEN2GDS(pgen_fn, out.gdsfn="test.gds")
## PLINK2 PGEN to SeqArray GDS:
##     pgen file (14.3K):
##         plink2_gen.pgen
##     pvar file (12.7K):
##         plink2_gen.pvar
##     psam file (34.3K):
##         plink2_gen.psam
##         reading ...
##     # of samples: 2504
##     # of variants: 482
##     Output:
##         test.gds
## ...

# Format conversion from GDS to PGEN (pgen, pvar and psam files)
seqGDS2PGEN("test.gds", "test_out")
## SeqArray GDS to PLINK2 PGEN:
##     open 'test.gds'
##     # of samples: 2,504
##     # of variants: 482
##     [Output]
##     PSAM: test_out.psam
##     PVAR: test_out.pvar
##     PGEN: test_out.pgen
## ...

The pgen writer stores each variant record in the smallest of the dense 2-bit, 1-bit and difference-list encodings (with multiallelic and phase tracks), following the thresholds used by PLINK2, but it does not use the LD-based encodings of PLINK2. The output can therefore be slightly larger than a pgen file written by PLINK2 itself; run plink2 --pfile test_out --make-pgen --out new if the smallest file size is needed.

Also See

seqVCF2GDS() in the SeqArray package, conversion from VCF files to GDS files.

seqBED2GDS() in the SeqArray package, conversion from PLINK BED files to GDS files.

seqBGEN2GDS() conversion from BGEN files to GDS files.