snpgdsBED2GDS {SNPRelate}R Documentation

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

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).

Value

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

Author(s)

Xiuwen Zheng

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/

See Also

snpgdsOption, snpgdsPED2GDS, snpgdsGDS2PED

Examples

# 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)
[Package SNPRelate version 1.10.2 Index]