ligerCommand-class

ligerCommand

show,ligerCommand-method

ligerCommand object: Record the input and time of a LIGER function call

Uses an extension of nonnegative matrix factorization to identify shared and dataset-specific factors. See Welch J, Kozareva V, et al (2019) <doi:10.1016/j.cell.2019.05.006>, and Liu J, Gao C, Sodicoff J, et al (2020) <doi:10.1038/s41596-020-0391-8> for more details.

Yichen Wang

rliger

Linked Inference of Genomic Experimental Relationships

Joshua Welch

Chao Gao

Jialin Liu

Joshua Sodicoff

Velina Kozareva

Evan Macosko

Paul Hoffman

Ilya Korsunsky

Robert Lee

Andrew Robbins

ligerCommand-class function

<dl><dt>object</dt>
<dd>A <code>ligerCommand</code> object</dd></dl>

Arguments

<dl>
<dt><code>funcName</code></dt>
<dd>Name of the function</dd></dl>
<dt><code>time</code></dt>
<dd>A time stamp object</dd>
<dt><code>call</code></dt>
<dd>A character string converted from system call</dd>
<dt><code>parameters</code></dt>
<dd>List of all arguments except the liger object.
Large object are summarized to short string.</dd>
<dt><code>objSummary</code></dt>
<dd>List of attributes of the liger object as a
snapshot when command is operated.</dd>
<dt><code>ligerVersion</code></dt>
<dd>Character string converted from
<code>packageVersion("rliger")</code>.</dd>
<dt><code>dependencyVersion</code></dt>
<dd>Named character vector of version number, if any
dependency library has a chance to be included by the function. A
dependency might only be invoked under certain conditions, such as using
an alternative algorithm, which a call does not actually reach to, but it
would still be included for this call.</dd>

Slots

ligerCommand object: Record the input and time of a LIGER function call — ligerCommand-class

<dl>

<dt>object</dt>
<dd>A <code>ligerCommand</code> object</dd>

</dl>

<dl>
<dt><code>funcName</code></dt>
<dd>Name of the function</dd>


<dt><code>time</code></dt>
<dd>A time stamp object</dd>


<dt><code>call</code></dt>
<dd>A character string converted from system call</dd>


<dt><code>parameters</code></dt>
<dd>List of all arguments except the liger object.
Large object are summarized to short string.</dd>


<dt><code>objSummary</code></dt>
<dd>List of attributes of the liger object as a
snapshot when command is operated.</dd>


<dt><code>ligerVersion</code></dt>
<dd>Character string converted from
<code>packageVersion("rliger")</code>.</dd>


<dt><code>dependencyVersion</code></dt>
<dd>Named character vector of version number, if any
dependency library has a chance to be included by the function. A
dependency might only be invoked under certain conditions, such as using
an alternative algorithm, which a call does not actually reach to, but it
would still be included for this call.</dd>


</dl>

ligerCommand-class: ligerCommand object: Record the input and time of a LIGER function call

Description

Usage

Arguments

Slots

Examples