readBED

prefix of PLINK file set, or the fullname of a BED file.

the row names: 1 = use individual ID, 2 = family and individual
ID, def = NULL.

the column names: 1 = use variant ID (i.e., rsID), 2 = CHR:POS, 3
= CHR:POS_A1_A2

suppress screen printing? (def=TRUE)

quiet

Read a BED file into a R matrix. This is meant for in-of-memory process of moderate
to small sized genotype.

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

readBED function

<dl><dt>pfx</dt>
<dd>prefix of PLINK file set, or the fullname of a BED file.</dd>
<dt>row</dt>
<dd>the row names: 1 = use individual ID, 2 = family and individual
ID, def = NULL.</dd>
<dt>col</dt>
<dd>the column names: 1 = use variant ID (i.e., rsID), 2 = CHR:POS, 3
= CHR:POS_A1_A2</dd>
<dt>quiet</dt>
<dd>suppress screen printing? (def=TRUE)</dd></dl>

Arguments

Read BED file — readBED

<dl>

<dt>pfx</dt>
<dd>prefix of PLINK file set, or the fullname of a BED file.</dd>


<dt>row</dt>
<dd>the row names: 1 = use individual ID, 2 = family and individual
ID, def = NULL.</dd>


<dt>col</dt>
<dd>the column names: 1 = use variant ID (i.e., rsID), 2 = CHR:POS, 3
= CHR:POS_A1_A2</dd>


<dt>quiet</dt>
<dd>suppress screen printing? (def=TRUE)</dd>

</dl>

readBED: Read BED file

Description

Usage

Value

Arguments

Details

See Also

Examples