Neighbor-class

Neighbor

The Neighbor class is used to store the results of neighbor finding
algorithms

Defines S4 classes for single-cell genomic data and associated
information, such as dimensionality reduction embeddings, nearest-neighbor
graphs, and spatially-resolved coordinates. Provides data access methods and
R-native hooks to ensure the Seurat object is familiar to other R users. 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>,
and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
more details.

Paul Hoffman

SeuratObject

Data Structures for Single Cell Data

Rahul Satija

David Collins

Yuhan Hao

Austin Hartman

Gesmira Molla

Andrew Butler

Tim Stuart

Madeline Kowalski

Saket Choudhary

Skylar Li

Longda Jiang

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

Neighbor-class function

<dl>
<dt><code>nn.idx</code></dt>
<dd>Matrix containing the nearest neighbor indices</dd></dl>
<dt><code>nn.dist</code></dt>
<dd>Matrix containing the nearest neighbor distances</dd>
<dt><code>alg.idx</code></dt>
<dd>The neighbor finding index (if applicable). E.g. the annoy
index</dd>
<dt><code>alg.info</code></dt>
<dd>Any information associated with the algorithm that may be
needed downstream (e.g. distance metric used with annoy is needed when
reading in from stored file).</dd>
<dt><code>cell.names</code></dt>
<dd>Names of the cells for which the neighbors have been
computed.</dd>

Slots

The Neighbor class — Neighbor-class

<dl>
<dt><code>nn.idx</code></dt>
<dd>Matrix containing the nearest neighbor indices</dd>


<dt><code>nn.dist</code></dt>
<dd>Matrix containing the nearest neighbor distances</dd>


<dt><code>alg.idx</code></dt>
<dd>The neighbor finding index (if applicable). E.g. the annoy
index</dd>


<dt><code>alg.info</code></dt>
<dd>Any information associated with the algorithm that may be
needed downstream (e.g. distance metric used with annoy is needed when
reading in from stored file).</dd>


<dt><code>cell.names</code></dt>
<dd>Names of the cells for which the neighbors have been
computed.</dd>


</dl>

The Neighbor class

Neighbor-class: The Neighbor class

Description

Arguments

Slots