snpgdsGEN2GDS {SNPRelate} | R Documentation

## 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

http://www.stats.ox.ac.uk/~marchini/software/gwas/file_format.html

### See Also

`snpgdsBED2GDS`, `snpgdsVCF2GDS`

### Examples

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

    ## End(Not run)

[Package SNPRelate version 1.12.2 Index]