emmax_kin: Estimate kinship with EMMAX

In OchoaLab/genbin: R wrappers for binaries in genetics

Estimate kinship with EMMAX

Description

Uses emmax-kin with default option to estimate the kinship matrix. The output file will be named name.BN.kinf using the input name below (emmax-kin does not allow the input and output names to be different).

Usage

emmax_kin(name, emmax_kin_bin = "emmax-kin", verbose = TRUE)

Arguments

name	The shared name of the input plink TPED/TFAM files without extensions.
emmax_kin_bin	The path to the binary executable. Default assumes emmax-kin is in the PATH.
verbose	If TRUE (default), prints the command line before it is executed.

Value

Nothing (the kinship matrix is not read in; see example below for reading with a different function).

See Also

genio::read_matrix() for reading plain-text matrices.

plink1_bed_to_tped() for creating TPED/TFAM files from BED/BIM/FAM files.

require_files_tped() for requiring that the TPED/TFAM files exist (used internally by emmax_kin).

delete_files_tped() for deleting TPED/TFAM files.

emmax_lmm() for running GWAS with EMMAX.

system3(), used (with ret = FALSE) for executing EMMAX and error handling.

Examples

## Not run: 
# create kinship matrix estimate (on file)
emmax_kin( name )

# read file with genio
kinship <- genio::read_matrix( name, ext = 'BN.kinf' )

## End(Not run)

OchoaLab/genbin documentation built on Nov. 14, 2024, 7:33 p.m.