createLigerDataset

Create in-memory ligerDataset object

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

createLigerDataset function

<dl><dt>rawData, normData, scaleData</dt>
<dd>A <code><a href="/link/dgCMatrix-class?package=rliger&version=2.0.1" data-mini-rdoc="rliger::dgCMatrix-class">dgCMatrix-class</a></code>
object for the raw or normalized expression count or a dense matrix of scaled
variable gene expression, respectively. Default <code>NULL</code> for all three but
at lease one has to be specified.</dd>
<dt>modal</dt>
<dd>Name of modality for this dataset. Currently options of
<code>"default"</code>, <code>"rna"</code>, <code>"atac"</code>, <code>"spatial"</code> and
<code>"meth"</code> are supported. Default <code>"default"</code>.</dd>
<dt>featureMeta</dt>
<dd>Data frame of feature metadata. Default <code>NULL</code>.</dd>
<dt>...</dt>
<dd>Additional slot data. See ligerDataset for detail.
Given values will be directly placed at corresponding slots.</dd></dl>

Arguments

Create in-memory ligerDataset object — createLigerDataset

<dl>

<dt>rawData, normData, scaleData</dt>
<dd>A <code><a href='https://rdrr.io/pkg/Matrix/man/dgCMatrix-class.html'>dgCMatrix-class</a></code>
object for the raw or normalized expression count or a dense matrix of scaled
variable gene expression, respectively. Default <code>NULL</code> for all three but
at lease one has to be specified.</dd>


<dt>modal</dt>
<dd>Name of modality for this dataset. Currently options of
<code>"default"</code>, <code>"rna"</code>, <code>"atac"</code>, <code>"spatial"</code> and
<code>"meth"</code> are supported. Default <code>"default"</code>.</dd>


<dt>featureMeta</dt>
<dd>Data frame of feature metadata. Default <code>NULL</code>.</dd>


<dt>...</dt>
<dd>Additional slot data. See ligerDataset for detail.
Given values will be directly placed at corresponding slots.</dd>

</dl>

Create in-memory ligerDataset object

createLigerDataset: Create in-memory ligerDataset object

Description

Usage

Arguments

See Also

Examples