DietSeurat

Keep only certain aspects of the Seurat object. Can be useful in functions that utilize merge as
it reduces the amount of data in the merge.

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

Christoph Hafemeister

Yuhan Hao

Austin Hartman

Jaison Jain

Madeline Kowalski

Efthymia Papalexi

Patrick Roelli

Rahul Satija

Karthik Shekhar

Avi Srivastava

Tim Stuart

Kristof Torkenczy

Shiwei Zheng

Satija Lab and Collaborators 

DietSeurat function

<dl><dt>object</dt>
<dd>Seurat object</dd>
<dt>counts</dt>
<dd>Preserve the count matrices for the assays specified</dd>
<dt>data</dt>
<dd>Preserve the data slot for the assays specified</dd>
<dt>scale.data</dt>
<dd>Preserve the scale.data slot for the assays specified</dd>
<dt>features</dt>
<dd>Only keep a subset of features, defaults to all features</dd>
<dt>assays</dt>
<dd>Only keep a subset of assays specified here</dd>
<dt>dimreducs</dt>
<dd>Only keep a subset of DimReducs specified here (if NULL,
remove all DimReducs)</dd>
<dt>graphs</dt>
<dd>Only keep a subset of Graphs specified here (if NULL, remove
all Graphs)</dd>
<dt>misc</dt>
<dd>Preserve the <code>misc</code> slot; default is <code>TRUE</code></dd></dl>

Arguments

Slim down a Seurat object — DietSeurat

<dl>

<dt>object</dt>
<dd>Seurat object</dd>


<dt>counts</dt>
<dd>Preserve the count matrices for the assays specified</dd>


<dt>data</dt>
<dd>Preserve the data slot for the assays specified</dd>


<dt>scale.data</dt>
<dd>Preserve the scale.data slot for the assays specified</dd>


<dt>features</dt>
<dd>Only keep a subset of features, defaults to all features</dd>


<dt>assays</dt>
<dd>Only keep a subset of assays specified here</dd>


<dt>dimreducs</dt>
<dd>Only keep a subset of DimReducs specified here (if NULL,
remove all DimReducs)</dd>


<dt>graphs</dt>
<dd>Only keep a subset of Graphs specified here (if NULL, remove
all Graphs)</dd>


<dt>misc</dt>
<dd>Preserve the <code>misc</code> slot; default is <code>TRUE</code></dd>

</dl>

Slim down a Seurat object

DietSeurat: Slim down a Seurat object

Description

Usage

Arguments