Package 'pgen2gds'

Convert SeqArray GDS to PLINK2 PGEN files

Description

Converts a SeqArray GDS file to PLINK2 pgen, pvar and psam files.

Usage

seqGDS2PGEN(gdsfile, out.fn,
    write.rsid=c("auto", "annot_id", "chr_pos_ref_alt"),
    half.call=c("missing", "haploid"), use.phase=TRUE, chr_prefix="",
    verbose=TRUE)

Arguments

gdsfile	a SeqVarGDSClass object or a file name of SeqArray GDS
out.fn	the file name prefix of the output PLINK2 files; out.fn.pgen, out.fn.pvar and out.fn.psam are created
write.rsid	"auto": use annotation/id and fall back to "chr_pos_ref_alt" when the ID is missing or "."; "annot_id": use annotation/id only; "chr_pos_ref_alt": use "chromosome_position_ref_alt"
half.call	how to handle a genotype with one missing allele (a half call or a haploid call): "missing" (default) codes it as missing, "haploid" codes it as homozygous for the observed allele
use.phase	if TRUE, write the phase information of heterozygous genotypes to the pgen file
chr_prefix	the prefix of chromosome codes, e.g., "chr"; it can be used to restore the prefix removed by ignore.chr.prefix in seqPGEN2GDS
verbose	if TRUE, show information

Details

The sample and variant selections set by seqSetFilter are respected, so seqGDS2PGEN() can export a subset of the GDS file. The ploidy has to be 2. Dosages are not exported.

The pgen file uses the PLINK2 storage mode 0x10. Each variant record is stored in the smallest of the dense 2-bit, 1-bit and difference-list encodings, following the thresholds used by PLINK2, and multiallelic genotypes and hardcall phase are stored in the corresponding auxiliary data tracks. The LD-based encodings of PLINK2 (differences from the previous variant) are not used, so the pgen file can be slightly larger than the file generated by PLINK2 itself, especially for datasets with many common variants in strong linkage disequilibrium. If the smallest file size is required, the files can be re-encoded by PLINK2, e.g., plink2 --pfile out.fn --make-pgen --out new.fn.

The pgen format keeps phase information for heterozygous genotypes only, so the phase flags of homozygous and haploid genotypes in the GDS file are ignored without loss of information.

The pvar file has the columns #CHROM, POS, ID, REF and ALT, where REF and ALT are taken from the GDS variable allele. If the chromosome codes are not recognized by PLINK2 (e.g., non-standard contig names), --allow-extra-chr may be needed when the files are loaded in PLINK2.

The psam file has the column IID from sample.id, and the columns FID, PAT, MAT, SEX and PHENO1 when the GDS variables sample.annotation/family, sample.annotation/father, sample.annotation/mother, sample.annotation/sex and sample.annotation/phenotype exist (the same variables as created by seqBED2GDS and seqPGEN2GDS).

Value

Return the file names of the pgen, pvar and psam files with absolute paths.

Author(s)

Xiuwen Zheng

References

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

See Also

seqPGEN2GDS, seqGDS2BED, seqGDS2VCF

Examples

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

# PGEN to GDS
seqPGEN2GDS(pgen_fn, out.gdsfn="test.gds")

# GDS to PGEN
seqGDS2PGEN("test.gds", "test_out")

head(seqReadPVAR("test_out.pvar"))

# delete the temporary files
unlink(c("test.gds", "test_out.pgen", "test_out.pvar", "test_out.psam"),
    force=TRUE)

---

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

Details

The sample IDs are taken from the column IID of the psam file. The psam columns FID, PAT, MAT and SEX are stored in the GDS variables sample.annotation/family, sample.annotation/father, sample.annotation/mother and sample.annotation/sex (coded as "M", "F" or "") if they exist, and the first phenotype column is stored in sample.annotation/phenotype (the same variables as created by seqBED2GDS). Dosages and phase information in the pgen file are not imported.

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

seqGDS2PGEN, 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, seqGDS2PGEN

Examples

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

head(seqReadPVAR(pvar_fn))

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