snpgdsPED2GDS: Conversion from PLINK PED to GDS

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

Description

Convert a PLINK PED text file to a GDS file.

Usage

snpgdsPED2GDS(ped.fn, map.fn, out.gdsfn, family=TRUE, snpfirstdim=FALSE,
    compress.annotation="ZIP_RA.max", compress.geno="", verbose=TRUE)

Arguments

ped.fn	the file name of PED file, genotype information
map.fn	the file name of MAP file
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)
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
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.

PED – PLINK PED format.

Value

None.

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

snpgdsGDS2PED, snpgdsBED2GDS, snpgdsGDS2BED

Examples

# open
genofile <- snpgdsOpen(snpgdsExampleFileName())

snpgdsGDS2PED(genofile, "tmp")

# close
snpgdsClose(genofile)


# PED ==> GDS
snpgdsPED2GDS("tmp.ped", "tmp.map", "test.gds")


# delete the temporary file
unlink(c("tmp.ped", "tmp.map", "test.gds"), force=TRUE)

Example output

Loading required package: gdsfmt
SNPRelate -- supported by Streaming SIMD Extensions 2 (SSE2)
Converting from GDS to PLINK PED:
	Output a MAP file DONE.
	Output a PED file ...
		Output: 	Fri Jan 12 11:11:11 2018	0%
		Output: 	Fri Jan 12 11:11:12 2018	100%
PLINK PED/MAP to GDS Format:
Import 9088 variants from 'tmp.map'
Chromosome:
  1  10  11  12  13  14  15  16  17  18  19   2  20  21  22   3   4   5   6   7 
716 483 447 427 344 282 262 278 207 266 120 742 229 126 116 609 562 566 565 472 
  8   9   X 
488 416 365 
Reading 'tmp.ped'
Output: 'test.gds'
Import 279 samples
Transpose the genotypic matrix ...
Done.
Optimize the access efficiency ...
Clean up the fragments of GDS file:
    open the file 'test.gds' (1.3M)
    # of fragments: 50
    save to 'test.gds.tmp'
    rename 'test.gds.tmp' (711.4K, reduced: 618.7K)
    # of fragments: 26

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