prep_LDAK_Kinship: Prepare a Kinship matrix for use with LDAK

In deruncie/GridLMM: Efficient Mixed Models for GWAS with multiple Random Effects

Prepare a Kinship matrix for use with LDAK

Description

Takes an R matrix and saves it to disk in a format that LDAK can use

Usage

prep_LDAK_Kinship(K, kinfile, LDAK_program = "LDAK/ldak5")

Arguments

K	A matrix. Must have rownames.
kinfile	The base of the filename fo the kinship files to be created, including path.
LDAK_program	The path to the LDAK program

Details

The matrix is first saved as a text file (without row/column names), and then LDAK is called by system with option "–convert-raw" to convert it into the format used by LDAK. Temporary files are removed. The .grn.id file contains the rownames of K repeated in two columns.

Value

A character with the base file name of the converted matrix.

deruncie/GridLMM documentation built on July 3, 2025, 6:32 p.m.