Package 'pgen2gds'

Title: Format Conversion from PLINK2 PGEN to GDS
Description: Provides functions for the format conversion from PLINK2 pgen files to SeqArray GDS files.
Authors: Xiuwen Zheng [aut, cre] (ORCID: <https://orcid.org/0000-0002-1390-0708>)
Maintainer: Xiuwen Zheng <[email protected]>
License: GPL-3
Version: 0.99.2
Built: 2026-06-06 10:06:47 UTC
Source: https://github.com/BiocStaging/pgen2gds

Help Index

Reformat PLINK2 PGEN files

Description

Reformats PLINK2 pgen files to GDS format.

Usage

seqPGEN2GDS(pgen.fn, pvar.fn=NULL, psam.fn=NULL, out.gdsfn,
    compress.geno="LZMA_RA", compress.annot="LZMA_RA", variant.sel=NULL,
    sample.sel=NULL, start=1L, count=NA_integer_,
    ignore.chr.prefix=c("chr", "0"), reference=NULL, optimize=TRUE,
    digest=TRUE, parallel=FALSE, balancing=TRUE, verbose=TRUE)

Arguments

pgen.fn

a file name for the pgen file
pvar.fn

a file name for the pvar file, or NULL to use the default
psam.fn

a file name for the psam file, or NULL to use the default
out.gdsfn

the file name of output GDS file
compress.geno

the compression method for "genotype"; optional values are defined in the function add.gdsn
compress.annot

the compression method for the GDS variables, except "genotype"; optional values are defined in the function add.gdsn
variant.sel

NULL for no variant selection, a logical vector or a numeric vector to specify the variant selection
sample.sel

NULL for no sample selection, a logical vector or a numeric vector to specify the sample selection
start

the starting variant if importing part of the pgen file
count

the maximum count of variant if importing part of the pgen file, NA_integer_ or any non-positive value indicates importing to the end
ignore.chr.prefix

a vector of character, indicating the prefix of chromosome which should be ignored, e.g., "chr"; it is not case-sensitive
reference

genome reference, like "GRCh37", "GRCh38"; it is not specified if reference=NULL
optimize

if TRUE, optimize the access efficiency by calling cleanup.gds
digest

a logical value (TRUE/FALSE) or a character (e.g., "md5"); add hash codes to the GDS file if TRUE or a digest algorithm is specified
parallel

FALSE (serial processing), TRUE (parallel processing), a numeric value indicating the number of cores, or a cluster object for parallel processing; parallel is passed to the argument cl in seqParallel, see seqParallel for more details
balancing

whether to perform workload balancing or not, only applicable when multiple cores are used; if NA, use TRUE as a default until getOption("seqarray.balancing") is set and not TRUE
verbose

if TRUE, show information

Value

Return the file name of SeqArray GDS file with an absolute path.

Author(s)

Xiuwen Zheng

References

https://www.cog-genomics.org/plink/2.0/

See Also

seqReadPVAR

Examples

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

seqPGEN2GDS(pgen_fn, out.gdsfn="test.gds")

# delete the temporary file
unlink("test.gds", force=TRUE)

Read PLINK2 pvar file

Description

Read PLINK2 pvar file for variants

Usage

seqReadPVAR(pvar, sel=NULL)

Arguments

pvar

a file name of a pvar file (from NewPvar), or a pvar object, which can be queried for variant IDs and allele codes
sel

NULL, a logical vector or a numeric vector for specifying the variants; NULL for including all variants

Value

Return a data frame with the columns chrom, pos, allele and rsid.

Author(s)

Xiuwen Zheng

References

https://www.cog-genomics.org/plink/2.0/

See Also

seqPGEN2GDS

Examples

pvar_fn <- system.file("extdata", "plink2_gen.pvar", package="pgen2gds")

head(seqReadPVAR(pvar_fn))