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>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details. Please note: SDMTools is available is available from the CRAN archives with install.packages("https://cran.rstudio.com//src/contrib/Archive/SDMTools/SDMTools_1.1-221.2.tar.gz", repos = NULL); it is not in the standard repositories.

Paul Hoffman

Seurat

Tools for Single Cell Genomics

Rahul Satija

Andrew Butler

Tim Stuart

Jeff Farrell

Shiwei Zheng

Christoph Hafemeister

Patrick Roelli

Yuhan Hao

IntegrationData-class function

<dl class="dl-horizontal">
<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

The IntegrationData Class

IntegrationData-class: The IntegrationData Class

Description

Arguments

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