SeqArray (version 1.10.1)

seqBED2GDS: Convert PLINK BED Format to SeqArray Format

Description

Converts a PLINK BED file to a sequence GDS file.

Usage

seqBED2GDS(bed.fn, fam.fn, bim.fn, out.gdsfn, compress.geno="ZIP_RA", compress.annotation="ZIP_RA", optimize=TRUE, verbose=TRUE)

Arguments

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

out.gdsfn

the file name, output a file of SeqArray format

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

optimize

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

verbose

if TRUE, show information

Value

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

See Also

seqSNP2GDS, seqVCF2GDS

Examples

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

seqSummary("tmp.gds")

# remove the temporary file
unlink("tmp.gds", force=TRUE)