snpgdsBED2GDS: Conversion from PLINK BED to GDS

Description

Convert a PLINK binary ped file to a GDS file.

Usage

snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, out.gdsfn, family=FALSE, snpfirstdim=NA, compress.annotation="ZIP_RA.max", compress.geno="", option=NULL, cvt.chr=c("int", "char"), cvt.snpid=c("auto", "int"), 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 output GDS file

family

if TRUE, to include family information in the sample annotation

snpfirstdim

if TRUE, genotypes are stored in the individual-major mode, (i.e, list all SNPs for the first individual, and then list all SNPs for the second individual, etc); NA, the dimension is determined by the BED file

compress.annotation

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

compress.geno

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

option

NULL or an object from snpgdsOption, see details

cvt.chr

"int" -- chromosome code in the GDS file is integer; "char" -- chromosome code in the GDS file is character

cvt.snpid

"int" -- to create an integer snp.id starting from 1; "auto" -- if SNP IDs in the PLINK file are not unique, to create an an integer snp.id, otherwise to use SNP IDs for snp.id

verbose

if TRUE, show information

Value

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

Details

GDS -- Genomic Data Structures, the extended file name used for storing genetic data, and the file format is used in the gdsfmt package.

BED -- the PLINK binary ped format.

The user could use option to specify the range of code for autosomes. For humans there are 22 autosomes (from 1 to 22), but dogs have 38 autosomes. Note that the default settings are used for humans. The user could call option = snpgdsOption(autosome.end=38) for importing the BED file of dog. It also allow define new chromosome coding, e.g., option = snpgdsOption(Z=27).

References

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC. 2007. PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.

http://corearray.sourceforge.net/

Examples

Run this code

# 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
snpgdsBED2GDS(bed.fn, fam.fn, bim.fn, "HapMap.gds")

# open
genofile <- snpgdsOpen("HapMap.gds")
genofile

# close
snpgdsClose(genofile)


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

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