ReadHardcalls

This function treats the data as diploid; you can divide by 2, and then
treat 0.5 as NA, if it's actually haploid.

A thin wrapper over PLINK 2's core libraries which provides an R
interface for reading .pgen files.  A minimal .pvar loader is also
included.  Chang et al. (2015) \doi{10.1186/s13742-015-0047-8}.

Christopher Chang

pgenlibr

PLINK 2 Binary (.pgen) Reader

Eric Biggers

Yann Collet

Meta Platforms, Inc. 

Evan Nemerson

Przemyslaw Skibinski

Nick Terrell

ReadHardcalls function

<dl><dt>pgen</dt>
<dd>Object returned by NewPgen().</dd>
<dt>buf</dt>
<dd>Buffer returned by Buf() or IntBuf().</dd>
<dt>variant_num</dt>
<dd>Variant index (1-based).</dd>
<dt>allele_num</dt>
<dd>Allele index; 1 corresponds to REF, 2 to the first ALT
allele, 3 to the second ALT allele if it exists, etc. Optional, defaults
2.</dd></dl>

Arguments

Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA}
values indicating the number of copies of the first ALT (or user-specified)
allele each sample has. — ReadHardcalls

<dl>

<dt>pgen</dt>
<dd>Object returned by NewPgen().</dd>


<dt>buf</dt>
<dd>Buffer returned by Buf() or IntBuf().</dd>


<dt>variant_num</dt>
<dd>Variant index (1-based).</dd>


<dt>allele_num</dt>
<dd>Allele index; 1 corresponds to REF, 2 to the first ALT
allele, 3 to the second ALT allele if it exists, etc. Optional, defaults
2.</dd>

</dl>

Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA}
values indicating the number of copies of the first ALT (or user-specified)
allele each sample has.

ReadHardcalls: Loads the variant_numth variant, and then fills buf with {0, 1, 2, NA} values indicating the number of copies of the first ALT (or user-specified) allele each sample has.

Description

Usage

Value

Arguments