snpgdsBED2GDS

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Conversion from PLINK BED to GDS

Convert a PLINK binary ped file to a GDS file.

Keywords
GWAS, GDS
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.

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

Aliases
  • snpgdsBED2GDS
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)
Documentation reproduced from package SNPRelate, version 1.6.4, License: GPL-3

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