snpgdsBED2GDS: Conversion from PLINK BED to GDS

In SNPRelate: Parallel Computing Toolset for Relatedness and Principal Component Analysis of SNP Data

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="LZMA_RA", 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"; if it is missing, ".fam" is added to bed.fn
bim.fn	the file name of extended MAP file: two extra columns = allele names; if it is missing, ".bim" is added to bim.fn
out.gdsfn	the output file name of 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.

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)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Start snpgdsBED2GDS ...
	BED file: "/usr/local/lib/R/site-library/SNPRelate/extdata/plinkhapmap.bed.gz" in the SNP-major mode (Sample X SNP)
	FAM file: "/usr/local/lib/R/site-library/SNPRelate/extdata/plinkhapmap.fam.gz", DONE.
	BIM file: "/usr/local/lib/R/site-library/SNPRelate/extdata/plinkhapmap.bim.gz", DONE.
Wed Nov 28 07:33:58 2018 	store sample id, snp id, position, and chromosome.
	start writing: 60 samples, 5000 SNPs ...
 	Wed Nov 28 07:33:58 2018	0%
 	Wed Nov 28 07:33:58 2018	100%
Wed Nov 28 07:33:58 2018 	Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'HapMap.gds' (104.6K)
    # of fragments: 38
    save to 'HapMap.gds.tmp'
    rename 'HapMap.gds.tmp' (104.4K, reduced: 240B)
    # of fragments: 18
File: /work/tmp/HapMap.gds (104.4K)
+    [  ] *
|--+ sample.id   { Str8 60 ZIP_ra(38.1%), 190B }
|--+ snp.id   { Int32 5000 ZIP_ra(36.2%), 7.1K }
|--+ snp.position   { Int32 5000 ZIP_ra(95.1%), 18.6K }
|--+ snp.chromosome   { UInt8 5000 ZIP_ra(1.82%), 98B } *
|--+ snp.allele   { Str8 5000 ZIP_ra(16.7%), 3.3K }
|--+ genotype   { Bit2 60x5000, 73.2K } *
\--+ sample.annot   [ data.frame ] *
   |--+ sex   { Str8 60 ZIP_ra(36.7%), 29B }
   \--+ phenotype   { Int32 60 ZIP_ra(10.8%), 33B }

SNPRelate documentation built on Nov. 8, 2020, 5:31 p.m.