seqBED2GDS: Conversion between PLINK BED and SeqArray GDS
In SeqArray: Data management of large-scale whole-genome sequence variant calls

Description Usage Arguments Value Author(s) See Also Examples

Conversion between PLINK BED format and SeqArray GDS format.

seqBED2GDS(bed.fn, fam.fn, bim.fn, out.gdsfn, compress.geno="LZMA_RA",
    compress.annotation="LZMA_RA", chr.conv=TRUE, optimize=TRUE, digest=TRUE,
    parallel=FALSE, verbose=TRUE)
seqGDS2BED(gdsfile, out.fn, multi.row=FALSE, verbose=TRUE)

`bed.fn`	the file name of binary file, genotype information
`fam.fn`	the file name of first six columns of `".ped"`
`bim.fn`	the file name of extended MAP file: two extra columns = allele names
`gdsfile`	character (a GDS file name), or a `SeqVarGDSClass` object
`out.gdsfn`	the file name, output a file of SeqArray format
`out.fn`	the file name of PLINK binary format without extended names
`compress.geno`	the compression method for "genotype"; optional values are defined in the function `add.gdsn`
`compress.annotation`	the compression method for the GDS variables, except "genotype"; optional values are defined in the function `add.gdsn`
`chr.conv`	if `TRUE`, convert numeric chromosome codes 23 to X, 24 to Y, 25 to XY, and 26 to MT
`optimize`	if `TRUE`, optimize the access efficiency by calling `cleanup.gds`
`digest`	a logical value (TRUE/FALSE) or a character ("md5", "sha1", "sha256", "sha384" or "sha512"); 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
`multi.row`	if `TRUE`, a multiallelic site is converted to multiple rows in PLINK bim and bed files
`verbose`	if `TRUE`, show information

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

Xiuwen Zheng

seqSNP2GDS, seqVCF2GDS

library(SNPRelate)

# PLINK BED files
bed.fn <- system.file("extdata", "plinkhapmap.bed.gz", package="SNPRelate")
fam.fn <- system.file("extdata", "plinkhapmap.fam.gz", package="SNPRelate")
bim.fn <- system.file("extdata", "plinkhapmap.bim.gz", package="SNPRelate")

# convert bed to gds
seqBED2GDS(bed.fn, fam.fn, bim.fn, "tmp.gds")

seqSummary("tmp.gds")


# convert gds to bed
gdsfn <- seqExampleFileName("gds")
seqGDS2BED(gdsfn, "plink")


# remove the temporary file
unlink(c("tmp.gds", "plink.fam", "plink.bim", "plink.bed"), force=TRUE)