initialize,BGData-method

The <a href="/link/?package=BGData&version=2.1.0" bgdata'="" data-mini-rdoc="BGData::"></a>'>BGData instance to be initialized. This argument
is passed in by R and can be ignored, but still needs to be documented.

.Object

A <a href="/link/?package=BGData&version=2.1.0" geno'="" data-mini-rdoc="BGData::"></a>'>geno object that contains genotypes. <a href="/link/?package=BGData&version=2.1.0" geno'="" data-mini-rdoc="BGData::"></a>'>geno is a
class union of several matrix-like types, many of them suitable for very
large datasets. Currently supported are <a rd-options="LinkedMatrix:LinkedMatrix-class" href="/link/LinkedMatrix%3A%3ALinkedMatrix?package=BGData&version=2.1.0&to=LinkedMatrix%3ALinkedMatrix-class" data-mini-rdoc="LinkedMatrix:LinkedMatrix-class::LinkedMatrix::LinkedMatrix">LinkedMatrix::LinkedMatrix</a>,
<a rd-options="BEDMatrix:BEDMatrix-class" href="/link/BEDMatrix%3A%3ABEDMatrix?package=BGData&version=2.1.0&to=BEDMatrix%3ABEDMatrix-class" data-mini-rdoc="BEDMatrix:BEDMatrix-class::BEDMatrix::BEDMatrix">BEDMatrix::BEDMatrix</a>, <a rd-options="bigmemory:big.matrix-class" href="/link/bigmemory%3A%3Abig.matrix?package=BGData&version=2.1.0&to=bigmemory%3Abig.matrix-class" data-mini-rdoc="bigmemory:big.matrix-class::bigmemory::big.matrix">bigmemory::big.matrix</a>, <code>ff_matrix</code>,
and <code>matrix</code>.

geno

A <code>data.frame</code> that contains phenotypes. A stub that only
contains an <code>IID</code> column populated with the rownames of <code>@geno</code> will be
generated if missing.

pheno

A <code>data.frame</code> that contains a genetic map. A stub that only
contains a <code>mrk</code> column populated with the colnames of <code>@geno</code> will be
generated if missing.

This method is run when a <a href="/link/?package=BGData&version=2.1.0" bgdata'="" data-mini-rdoc="BGData::"></a>'>BGData object is created using
<code>BGData(...)</code> or <code>new("BGData", ...)</code>.

An umbrella package providing a phenotype/genotype data structure
and scalable and efficient computational methods for large genomic datasets
in combination with several other packages: 'BEDMatrix', 'LinkedMatrix',
and 'symDMatrix'.

Alexander Grueneberg

BGData

A Suite of Packages for Analysis of Big Genomic Data

Gustavo de los Campos

Paulino Perez

Ana Vazquez

initialize,BGData-method function

The <a href='<a href='BGData'></a>'>BGData</a> instance to be initialized. This argument
is passed in by R and can be ignored, but still needs to be documented.

A <a href='<a href='geno'></a>'>geno</a> object that contains genotypes. <a href='<a href='geno'></a>'>geno</a> is a
class union of several matrix-like types, many of them suitable for very
large datasets. Currently supported are <a rd-options='LinkedMatrix:LinkedMatrix-class' href='LinkedMatrix::LinkedMatrix'>LinkedMatrix::LinkedMatrix</a>,
<a rd-options='BEDMatrix:BEDMatrix-class' href='BEDMatrix::BEDMatrix'>BEDMatrix::BEDMatrix</a>, <a rd-options='bigmemory:big.matrix-class' href='bigmemory::big.matrix'>bigmemory::big.matrix</a>, <code>ff_matrix</code>,
and <code>matrix</code>.

This method is run when a <a href='<a href='BGData'></a>'>BGData</a> object is created using
<code>BGData(...)</code> or <code>new("BGData", ...)</code>.

initialize,BGData-method: Creates a New BGData Instance.

Description

Usage

Arguments