readBSM {plinkFile}

Read Binary Symmetric Matrix (BSM)

Description

Read BSM represented by a pair of files suffixed by ".bin" and ".id", usually produced by PLINK and GCTA.

Usage

readBSM(pfx, dgv = 1, fid = NULL, id = NULL, bin = NULL)

Arguments

pfx

prefix of data files pfx.id and pfx.bin

dgv

diagonal value for matrix without a diagonal (def=1.0)

fid

separator between FID and IID (def=NULL, use IID only)

id

use id file instead of the default pfx.id

bin

use bin file instead of the default pfx.bin

Details

The ".bin" is a binary file storing the matrix entries, which can be

SQR

the N x N symmetric matrix in full

LWD

the lower triangle with diagonal

LND

the lower triangle without diagonal

, saved as either single or double precision.

The ".id" is a text file of N family ID (FID) and individual ID (IID) in two columns. By default, IID is used as matix row and column names.

PLINK option --make-red bin, --distance bin, and GCTA option --make-grm all creats binary symmetric matrices, widely used in linear mixed model or kernel based models for genetics.

Value

symmetric matrix loaded, with sample ID as both row and column names.

Examples

pfx <- file.path(system.file("extdata", package="plinkFile"), "m20.rel")
(readBSM(pfx, fid=":"))