ReadAlleles

This function treats the data as diploid. If it's really haploid, you may
want to compare the two rows, and then treat samples where the allele codes
differ as missing values.

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

ReadAlleles function

<dl><dt>pgen</dt>
<dd>Object returned by NewPgen().</dd>
<dt>acbuf</dt>
<dd>Buffer returned by AlleleCodeBuf() or IntAlleleCodeBuf().</dd>
<dt>variant_num</dt>
<dd>Variant index (1-based).</dd>
<dt>phasepresent_buf</dt>
<dd>Buffer returned by BoolBuf(). Optional; if
provided, elements are set to true when the sample has known phase. Most
of these values will be TRUE even when the raw data is unphased, because
homozygous genotypes always have known phase. (Missing genotypes are
considered to have unknown phase.)</dd></dl>

Arguments

Loads the variant_numth variant, and then fills acbuf with integer allele
codes, where each column of the buffer corresponds to a sample.  An allele
code of 0 corresponds to the REF allele, 1 to the first ALT, 2 to the
second ALT, etc.  Missing hardcalls are represented by a pair of NA codes. — ReadAlleles

<dl>

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


<dt>acbuf</dt>
<dd>Buffer returned by AlleleCodeBuf() or IntAlleleCodeBuf().</dd>


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


<dt>phasepresent_buf</dt>
<dd>Buffer returned by BoolBuf(). Optional; if
provided, elements are set to true when the sample has known phase. Most
of these values will be TRUE even when the raw data is unphased, because
homozygous genotypes always have known phase. (Missing genotypes are
considered to have unknown phase.)</dd>

</dl>

Loads the variant_numth variant, and then fills acbuf with integer allele
codes, where each column of the buffer corresponds to a sample.  An allele
code of 0 corresponds to the REF allele, 1 to the first ALT, 2 to the
second ALT, etc.  Missing hardcalls are represented by a pair of NA codes.

Description

Usage

Value

Arguments