kin2gds {GENESIS} | R Documentation

## Store kinship matrix in GDS

### Description

`kin2gds` and `mat2gds` write kinship matrices to GDS files.

### Usage

    kin2gds(ibdobj, gdsfile)
    mat2gds(mat, gdsfile)

### Arguments

`ibdobj` | A list with elements `sample.id` and `kinship`, such as the output of `snpgdsIBDKING`.
`mat` | A matrix with sample identifiers in colnames.
`gdsfile` | A character string with the name of the GDS file to create.

### Details

When using `pcair` or `pcairPartition` with large sample sizes, it can be more memory efficient to read data from GDS files. `kin2gds` and `mat2gds` store kinship matrices in GDS files for use with these functions.

### Author(s)

Stephanie M. Gogarten

### See Also

`kingToMatrix`, `snpgdsIBDKING`

### Examples

    library(gdsfmt)

    # KING results from the command-line program
    file.kin0 <- system.file("extdata", "MXL_ASW.kin0", package="GENESIS")
    file.kin <- system.file("extdata", "MXL_ASW.kin", package="GENESIS")
    KINGmat <- kingToMatrix(c(file.kin0, file.kin), estimator="Kinship")
    gdsfile <- tempfile()
    mat2gds(KINGmat, gdsfile)
    gds <- openfn.gds(gdsfile)
    gds
    closefn.gds(gds)

    # KING results from SNPRelate
    library(SNPRelate)
    geno <- snpgdsOpen(snpgdsExampleFileName())
    king <- snpgdsIBDKING(geno)
    closefn.gds(geno)
    kin2gds(king, gdsfile)
    gds <- openfn.gds(gdsfile)
    gds
    closefn.gds(gds)

[Package GENESIS version 2.22.2 Index]