AnchorSet-class

AnchorSet

The AnchorSet class is an intermediate data storage class that stores the anchors and other
related information needed for performing downstream analyses - namely data integration
(<code>IntegrateData</code>) and data transfer (<code>TransferData</code>).

A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.

Paul Hoffman

Seurat

Tools for Single Cell Genomics

Andrew Butler

Saket Choudhary

Charlotte Darby

Jeff Farrell

Isabella Grabski

Christoph Hafemeister

Yuhan Hao

Austin Hartman

Jaison Jain

Longda Jiang

Madeline Kowalski

Skylar Li

Gesmira Molla

Efthymia Papalexi

Patrick Roelli

Rahul Satija

Karthik Shekhar

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Shiwei Zheng

Satija Lab and Collaborators 

AnchorSet-class function

<dl>
<dt><code>object.list</code></dt>
<dd>List of objects used to create anchors</dd></dl>
<dt><code>reference.cells</code></dt>
<dd>List of cell names in the reference dataset - needed when performing data
transfer.</dd>
<dt><code>reference.objects</code></dt>
<dd>Position of reference object/s in object.list</dd>
<dt><code>query.cells</code></dt>
<dd>List of cell names in the query dataset - needed when performing data transfer</dd>
<dt><code>anchors</code></dt>
<dd>The anchor matrix. This contains the cell indices of both anchor pair cells, the
anchor score, and the index of the original dataset in the object.list for cell1 and cell2 of
the anchor.</dd>
<dt><code>offsets</code></dt>
<dd>The offsets used to enable cell look up in downstream functions</dd>
<dt><code>weight.reduction</code></dt>
<dd>The weight dimensional reduction used to calculate weight matrix</dd>
<dt><code>anchor.features</code></dt>
<dd>The features used when performing anchor finding.</dd>
<dt><code>neighbors</code></dt>
<dd>List containing Neighbor objects for reuse later (e.g. mapping)</dd>
<dt><code>command</code></dt>
<dd>Store log of parameters that were used</dd>

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The AnchorSet Class — AnchorSet-class

<dl>
<dt><code>object.list</code></dt>
<dd>List of objects used to create anchors</dd>


<dt><code>reference.cells</code></dt>
<dd>List of cell names in the reference dataset - needed when performing data
transfer.</dd>


<dt><code>reference.objects</code></dt>
<dd>Position of reference object/s in object.list</dd>


<dt><code>query.cells</code></dt>
<dd>List of cell names in the query dataset - needed when performing data transfer</dd>


<dt><code>anchors</code></dt>
<dd>The anchor matrix. This contains the cell indices of both anchor pair cells, the
anchor score, and the index of the original dataset in the object.list for cell1 and cell2 of
the anchor.</dd>


<dt><code>offsets</code></dt>
<dd>The offsets used to enable cell look up in downstream functions</dd>


<dt><code>weight.reduction</code></dt>
<dd>The weight dimensional reduction used to calculate weight matrix</dd>


<dt><code>anchor.features</code></dt>
<dd>The features used when performing anchor finding.</dd>


<dt><code>neighbors</code></dt>
<dd>List containing Neighbor objects for reuse later (e.g. mapping)</dd>


<dt><code>command</code></dt>
<dd>Store log of parameters that were used</dd>


</dl>

The AnchorSet Class

AnchorSet-class: The AnchorSet Class

Description

Arguments

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