readBSM

prefix of data files pfx.id and pfx.bin

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

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

use id file instead of the default <code>{pfx}.id</code>

use bin file instead of the default <code>{pfx}.bin</code>

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

Provide function that reads binary genotype produced by 'PLINK' <https://www.cog-genomics.org/plink/1.9/input#bed> into a R matrix, or scan the genotype one variant at a time like apply(), it also provides functions that reads and writes genotype relatedness/kinship matrices created by 'PLINK' <https://www.cog-genomics.org/plink/1.9/distance#make_rel> or 'GCTA' <https://cnsgenomics.com/software/gcta/#MakingaGRM>. Currently it does not support writing back into 'PLINK' binary, it is best used for bringing data produced by 'PLINK' and 'GCTA' into R environment.

Xiaoran Tong

plinkFile

'PLINK' (and 'GCTA') File Helpers

readBSM function

<dl><dt>pfx</dt>
<dd>prefix of data files pfx.id and pfx.bin</dd>
<dt>dgv</dt>
<dd>diagonal value for matrix without a diagonal (def=1.0)</dd>
<dt>fid</dt>
<dd>separator between FID and IID (def=NULL, use IID only)</dd>
<dt>id</dt>
<dd>use id file instead of the default <code>{pfx}.id</code></dd>
<dt>bin</dt>
<dd>use bin file instead of the default <code>{pfx}.bin</code></dd></dl>

Arguments

Read Binary Symmetric Matrix (BSM) — readBSM

<dl>

<dt>pfx</dt>
<dd>prefix of data files pfx.id and pfx.bin</dd>


<dt>dgv</dt>
<dd>diagonal value for matrix without a diagonal (def=1.0)</dd>


<dt>fid</dt>
<dd>separator between FID and IID (def=NULL, use IID only)</dd>


<dt>id</dt>
<dd>use id file instead of the default <code>{pfx}.id</code></dd>


<dt>bin</dt>
<dd>use bin file instead of the default <code>{pfx}.bin</code></dd>

</dl>

readBSM: Read Binary Symmetric Matrix (BSM)

Description

Usage

Value

Arguments

Details

Examples