readVCM

GRM (Genetic Relatedness Matrix) is the core formt of GCTA, which is a PLINK
binary symmetric matrix with an extra variant count matrix (VCM), this
function reads the VCM.

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

readVCM function

<dl><dt>pfx</dt>
<dd>prefix of GRM file set</dd>
<dt>fid</dt>
<dd>seperate after family ID (def=NULL, use IID only)</dd></dl>

Arguments

Read Variant Count Matrix (VCM) accompanying a GCTA GRM — readVCM

<dl>

<dt>pfx</dt>
<dd>prefix of GRM file set</dd>


<dt>fid</dt>
<dd>seperate after family ID (def=NULL, use IID only)</dd>

</dl>

readVCM: Read Variant Count Matrix (VCM) accompanying a GCTA GRM

Description

Usage

Value

Arguments

Examples