saveBED

Save a R matrix into a PLINK BED file.

Reads/write binary genotype file compatible with 'PLINK' <https://www.cog-genomics.org/plink/1.9/input#bed> into/from a R matrix; traverse genotype data one windows of variants at a time, like apply() or a for loop; reads/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> into/from a R square matrix. It is best used for bringing data produced by 'PLINK' and 'GCTA' into R workflow.

Xiaoran Tong

plinkFile

'PLINK' (and 'GCTA') File Helpers

saveBED function

<dl><dt>pfx</dt>
<dd>prefix of the output file set, in PLINK1 BED format.</dd>
<dt>bed</dt>
<dd>N x P genotype matrix</dd>
<dt>quiet</dt>
<dd>do not report (def=TRUE)</dd></dl>

Arguments

Save BED file — saveBED

<dl>

<dt>pfx</dt>
<dd>prefix of the output file set, in PLINK1 BED format.</dd>


<dt>bed</dt>
<dd>N x P genotype matrix</dd>


<dt>quiet</dt>
<dd>do not report (def=TRUE)</dd>

</dl>

saveBED: Save BED file

Description

Usage

Arguments

Details