IntegrationData-class

IntegrationData

The IntegrationData object is an intermediate storage container used internally throughout the
integration procedure to hold bits of data that are useful downstream.

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 

IntegrationData-class function

<dl>
<dt><code>neighbors</code></dt>
<dd>List of neighborhood information for cells (outputs of <code>RANN::nn2</code>)</dd></dl>
<dt><code>weights</code></dt>
<dd>Anchor weight matrix</dd>
<dt><code>integration.matrix</code></dt>
<dd>Integration matrix</dd>
<dt><code>anchors</code></dt>
<dd>Anchor matrix</dd>
<dt><code>offsets</code></dt>
<dd>The offsets used to enable cell look up in downstream functions</dd>
<dt><code>objects.ncell</code></dt>
<dd>Number of cells in each object in the object.list</dd>
<dt><code>sample.tree</code></dt>
<dd>Sample tree used for ordering multi-dataset integration</dd>

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The IntegrationData Class — IntegrationData-class

<dl>
<dt><code>neighbors</code></dt>
<dd>List of neighborhood information for cells (outputs of <code>RANN::nn2</code>)</dd>


<dt><code>weights</code></dt>
<dd>Anchor weight matrix</dd>


<dt><code>integration.matrix</code></dt>
<dd>Integration matrix</dd>


<dt><code>anchors</code></dt>
<dd>Anchor matrix</dd>


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


<dt><code>objects.ncell</code></dt>
<dd>Number of cells in each object in the object.list</dd>


<dt><code>sample.tree</code></dt>
<dd>Sample tree used for ordering multi-dataset integration</dd>


</dl>

The IntegrationData Class

IntegrationData-class: The IntegrationData Class

Description

Arguments

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