NewPgen

Opens a .pgen or PLINK 1 .bed file.

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

NewPgen function

<dl><dt>filename</dt>
<dd>.pgen/.bed file path.</dd>
<dt>pvar</dt>
<dd>Object (see NewPvar()) corresponding to the .pgen's companion
.pvar; technically optional, but necessary for some functionality. In
particular, at multiallelic variants, all ALT alleles may be collapsed
together when .pvar information is not available.</dd>
<dt>raw_sample_ct</dt>
<dd>Number of samples in file; required if it's a PLINK 1
.bed file, otherwise optional.</dd>
<dt>sample_subset</dt>
<dd>List of 1-based positions of samples to load;
optional, all samples are loaded if this is not specified.</dd></dl>

Arguments

Opens a .pgen or PLINK 1 .bed file. — NewPgen

<dl>

<dt>filename</dt>
<dd>.pgen/.bed file path.</dd>


<dt>pvar</dt>
<dd>Object (see NewPvar()) corresponding to the .pgen's companion
.pvar; technically optional, but necessary for some functionality. In
particular, at multiallelic variants, all ALT alleles may be collapsed
together when .pvar information is not available.</dd>


<dt>raw_sample_ct</dt>
<dd>Number of samples in file; required if it's a PLINK 1
.bed file, otherwise optional.</dd>


<dt>sample_subset</dt>
<dd>List of 1-based positions of samples to load;
optional, all samples are loaded if this is not specified.</dd>

</dl>

NewPgen: Opens a .pgen or PLINK 1 .bed file.

Description

Usage

Value

Arguments