snpgdsGEN2GDS: Conversion from Oxford GEN format to GDS

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

Conversion from Oxford GEN format to GDS

Description

Convert an Oxford GEN file (text format) to a GDS file.

Usage

snpgdsGEN2GDS(gen.fn, sample.fn, out.fn, chr.code=NULL,
    call.threshold=0.9, version=c(">=2.0", "<=1.1.5"),
    snpfirstdim=FALSE, compress.annotation="ZIP_RA.max", compress.geno="",
    verbose=TRUE)

Arguments

gen.fn	the file name of Oxford GEN text file(s), it could be a vector indicate merging all files
sample.fn	the file name of sample annotation
out.fn	the output GDS file
chr.code	a vector of chromosome code according to gen.fn, indicating chromosomes. It could be either numeric or character-type
call.threshold	the threshold to determine missing genotypes
version	either ">=2.0" or "<=1.1.5", see details
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.

NOTE : the sample file format (sample.fn) has changed with the release of SNPTEST v2. Specifically, the way in which covariates and phenotypes are coded on the second line of the header file has changed. version has to be specified, and the function uses ">=2.0" by default.

Value

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

Author(s)

Xiuwen Zheng

References

https://code.enkre.net/bgen

See Also

snpgdsBED2GDS, snpgdsVCF2GDS

Examples

cat("running snpgdsGEN2GDS ...\n")
## Not run: 
snpgdsGEN2GDS("test.gen", "test.sample", "output.gds", chr.code=1)

## End(Not run)

zhengxwen/SNPRelate documentation built on April 16, 2024, 8:42 a.m.