snpgdsBED2GDS {SNPRelate} | R Documentation

## Conversion from PLINK BED to GDS

### 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)

[Package SNPRelate version 1.18.1 Index]